diff --git a/scripts/ALE_reformat.py b/scripts/ALE_reformat.py
index 43f57de..0847f3c 100755
--- a/scripts/ALE_reformat.py
+++ b/scripts/ALE_reformat.py
@@ -5,7 +5,7 @@
 
 __author__    = "Cedric Chauve"
 __email__     = "cedric.chauve@sfu.ca"
-__version__   = "1.0"
+__version__   = "1.0.3"
 __status__    = "Released"
 
 import sys
@@ -38,16 +38,25 @@ def main():
     in_rec_xml_file = sys.argv[3]
     out_rec_xml_file = sys.argv[4]
 
+    # Creates a map from ALE species names to original species names
     species_map = newick_create_species_map(in_ale_species_tree, in_data_species_tree)
+    # Read an ALE recPhyloXML file
     tree = ET.parse(in_rec_xml_file)
+    # If the file includes an HGT, we do not create a reformatted file
     if not xml_check_transfer(tree, xml_ALE_identify_transfer):
+        # Rename species
         xml_rename_species(tree, species_map)
+        # Reformat losses
         xml_rename_losses(tree, xml_ALE_identify_loss, 'loss')
-        _ = xml_rename_ancestral_genes(tree, xml_ALE_identify_ancestral_gene, start_id=1)    
-        out_rec_xml_file_tmp = f'{out_rec_xml_file}_tmp'
-        tree.write(out_rec_xml_file_tmp)
-        _ = xml_reformat_file(out_rec_xml_file_tmp, out_rec_xml_file)
-        os.remove(out_rec_xml_file_tmp)
+        # Reformat ancestral gene names with integers ID starting at 1
+        _ = xml_rename_ancestral_genes(tree, xml_ALE_identify_ancestral_gene, start_id=1)
+        # Create a temporary recPhyloXML file
+        tmp_rec_file = f'{out_rec_xml_file}_tmp'
+        tree.write(tmp_rec_file)
+        # Reformat the temporary recPhyloXML file int the final recPhyloXML file
+        _ = xml_reformat_file(tmp_rec_file, out_rec_xml_file)
+        # Delete the temporary recPhyloXML file
+        os.remove(tmp_rec_file)
 
 if __name__ == "__main__":
     main()
diff --git a/scripts/DeCoSTAR_create_input_files.py b/scripts/DeCoSTAR_create_input_files.py
index 3742b00..f0a9922 100755
--- a/scripts/DeCoSTAR_create_input_files.py
+++ b/scripts/DeCoSTAR_create_input_files.py
@@ -5,35 +5,34 @@
 
 __author__    = "Cedric Chauve"
 __email__     = "cedric.chauve@sfu.ca"
-__version__   = "1.0"
+__version__   = "1.0.3"
 __status__    = "Released"
 
 import sys
 from data_utils import (
     data_gene2family,
-    data_species2gene_order_path,
-    data_family2reconciliation_path,
+    data_index2path,
     data_read_gene_order_file
 )
 
 ''' Read a gene order file and returns an order list of adjacencies strings '''
 def decostar_gene_order2adjacencies_str(
-        in_gene_order_file, in_gene2family_map, in_reconciled_families
+        in_gene_order_file, in_gene2family_map, in_families
 ):
     '''
     input: 
     - path to gene order file
     - map of gene to family ID
-    - list of reconciled families to consider 
-    (genes from other families are not accounted for)
+    - list of families to consider (genes from other families are not accounted for)
     output: list(str)
     '''
     orientation = {'1': '+', '0': '-'}
     adjacencies = []
     gene_order = data_read_gene_order_file(in_gene_order_file)
+    in_gene2family_keys = list(in_gene2family_map.keys())
     prev_gene = None
     for (gene_name,gene_chr,_,_,gene_sign) in gene_order:
-        if in_gene2family_map[gene_name] in in_reconciled_families:
+        if gene_name in in_gene2family_keys and in_gene2family_map[gene_name] in in_families:
             gene_orientation = orientation[gene_sign]
             if prev_gene is not None and prev_gene[1] == gene_chr:
                 adjacency = [
@@ -45,46 +44,44 @@ def decostar_gene_order2adjacencies_str(
     return adjacencies
 
 ''' 
-Creates the DeCoSTAR input gene trees distribution file 
-Compute a list of families for which the reconciled gene tree is available
+Creates the DeCoSTAR input (reconciled) gene trees distribution file 
+Compute a list of families for which the (reconciled) gene tree is provided
 '''
-def create_gene_distribution_file(in_reconciliations_file, out_trees_file):
+def decostar_create_gene_distribution_file(in_trees_file, out_trees_file):
     '''
     input: 
-    - dataset file with link from family to reconciled gene tree
+    - dataset file family<TAB>(reconciled) gene trees
     output: 
     - creates out_trees_file
-    - list(str) of families for which a reonciliation is available
+    - list(str) of families for which a (reconciled) gene tree is available
     '''
-    family2reconciliation_path = data_family2reconciliation_path(
-        in_reconciliations_file
-    )
-    reconciled_families = []
-    with open(out_trees_file, 'w') as trees:
-        for fam_id,reconciliation_file in family2reconciliation_path.items():
-            trees.write(f'{reconciliation_file}\n')
-            reconciled_families.append(fam_id)
-    return reconciled_families
+    family2trees_path = data_index2path(in_trees_file)
+    families = []
+    with open(out_trees_file, 'w') as out_trees:
+        for fam_id,trees_file in family2trees_path.items():
+            out_trees.write(f'{trees_file}\n')
+            families.append(fam_id)
+    return families
 
 ''' Creates the DeCoSTAR input adjacencies file '''
-def create_adjacencies_file(
-        in_gene_orders_file, in_families_file, in_reconciled_families,
+def decostar_create_adjacencies_file(
+        in_gene_orders_file, in_families_file, in_trees_families,
         out_adjacencies_file
 ):
     '''
     input: 
     - dataset file with link from species to gene order file
     - dataset families file
-    - list of reconciled families
+    - list of families with a (reconciled) tree provided as input
     output: 
     creates out_adjacencies_file
     '''
-    gene_order_files= data_species2gene_order_path(in_gene_orders_file)
+    gene_order_files= data_index2path(in_gene_orders_file)
     gene2family_map = data_gene2family(in_families_file)
     with open(out_adjacencies_file, 'w') as out_adjacencies:
         for species,gene_order_file in gene_order_files.items():
             species_adjacencies = decostar_gene_order2adjacencies_str(
-                gene_order_file, gene2family_map, in_reconciled_families            
+                gene_order_file, gene2family_map, in_trees_families            
             )
             for adjacency in species_adjacencies:
                 out_adjacencies.write(f'{adjacency}\n')
@@ -93,13 +90,17 @@ def create_adjacencies_file(
     
 def main():
     in_gene_orders_file = sys.argv[1]
-    in_reconciliations_file = sys.argv[2]
+    in_trees_file = sys.argv[2]
     in_families_file = sys.argv[3]
     out_adjacencies_file = sys.argv[4]
     out_trees_file = sys.argv[5]
 
-    reconciled_families = create_gene_distribution_file(in_reconciliations_file, out_trees_file)
-    create_adjacencies_file(in_gene_orders_file, in_families_file, reconciled_families, out_adjacencies_file)
+    # Creates the gene trees distribution file (reconciliations or samples of gene trees)
+    trees_families = decostar_create_gene_distribution_file(in_trees_file, out_trees_file)
+    # Creates the adjacencies file
+    decostar_create_adjacencies_file(
+        in_gene_orders_file, in_families_file, trees_families, out_adjacencies_file
+    )
         
 if __name__ == "__main__":
     main()
diff --git a/scripts/DeCoSTAR_ecceTERA_reformat.py b/scripts/DeCoSTAR_ecceTERA_reformat.py
index 0568aac..8ccf18f 100755
--- a/scripts/DeCoSTAR_ecceTERA_reformat.py
+++ b/scripts/DeCoSTAR_ecceTERA_reformat.py
@@ -5,14 +5,13 @@
 
 __author__    = "Cedric Chauve"
 __email__     = "cedric.chauve@sfu.ca"
-__version__   = "1.0"
+__version__   = "1.0.3"
 __status__    = "Released"
 
 import sys
 import os
 import xml.etree.ElementTree as ET
 
-
 from recPhyloXML_utils import xml_rename_species
 
 '''
@@ -25,11 +24,11 @@ def eccetera_read_results(in_genes_file1, in_genes_file2, sep='|'):
     input:
     - original and reformatted genes file
     output:
-    - dict(ecceTERA species -> data species)
-    - dict(ecceTERA family -> data family)
+    - dict(ecceTERA species -> original species)
+    - dict(ecceTERA family -> original family)
     '''
     species_dict,families_dict = {},{}
-    # Reading original genes
+    # Reading original DeCoSTAR genes
     data,data_idx = {},0
     with open(in_genes_file1, 'r') as in_genes:
         for gene_data in in_genes.readlines():
@@ -117,9 +116,9 @@ def eccetera_write_reconciliations(in_reconciliations_files, species_map, out_di
          out_reconciliation_file = os.path.join(out_dir, f'{family_id}{out_xml_ext}')
          tree.write(out_reconciliation_file)
          out_file.write(f'{family_id}\t{out_reconciliation_file}\n')
+         os.remove(tmp_rec_file)
             
 
-
 def main():
     in_genes_file1 = sys.argv[1] # DeCoSTAR genes file
     in_genes_file2 = sys.argv[2] # Reformatted genes file
@@ -129,11 +128,17 @@ def main():
     out_xml_ext = sys.argv[6] # Extension to recPhyloXML files
     out_reconciliations_file = sys.argv[7] # Data set reconciliations file
 
+    # Creates a map from DeCoSTAR species names to original species names
     species_map,families_map = eccetera_read_results(in_genes_file1, in_genes_file2)
+    # Read the species tree in XML format created by DeCoSTAR
     xml_sp_str = eccetera_read_species_tree(in_sp_xml_file)
+    # Creates one temporary recPhyloXML file per family extracted from the
+    # DeCoSTAR reocnciliations file
     tmp_reconciliations_files = eccetera_read_reconciliations(
         in_reconciliations_file, xml_sp_str, families_map, out_dir
     )
+    # Reformat the temporary rcPhyloXML files and writes a reconciliations file
+    # (<family><TAB><path to reconciliation file>)
     eccetera_write_reconciliations(
         tmp_reconciliations_files, species_map, out_dir, out_xml_ext, out_reconciliations_file
     )
diff --git a/scripts/DeCoSTAR_reformat.py b/scripts/DeCoSTAR_reformat.py
index 977e920..df97367 100755
--- a/scripts/DeCoSTAR_reformat.py
+++ b/scripts/DeCoSTAR_reformat.py
@@ -5,7 +5,7 @@
 
 __author__    = "Cedric Chauve"
 __email__     = "cedric.chauve@sfu.ca"
-__version__   = "1.0"
+__version__   = "1.0.3"
 __status__    = "Released"
 
 import sys
@@ -16,7 +16,7 @@
     data_create_equivalence_map,
     data_species_map,
     data_gene2family,
-    data_reconciliation_path2family
+    data_path2index
 )
 from recPhyloXML_utils import (
     xml_get_gene_tree_root,
@@ -71,7 +71,7 @@ def decostar_family_map(
     output:
     dict(str->str) from DeCoSTAR family ID to original family ID
     '''
-    reconciliation2family = data_reconciliation_path2family(
+    reconciliation2family = data_path2index(
         in_input_file
     )
     family_map = {}
@@ -326,9 +326,11 @@ def main():
     out_genes_file = sys.argv[9]
     out_adjacencies_dir = sys.argv[10]    
 
+    # Creates a map from DeCoSTAR species names to original species names
     species_map = decostar_species_map(
         in_species_file, in_decostar_species_file
     )
+    # Reformat the genes file created by DeCoSTAR to rename genes, families and species
     genes_map = decostar_reformat_genes(
         species_map,
         in_families_file, in_reconciliations_file,
@@ -336,6 +338,7 @@ def main():
         out_genes_file,
         already_reconciled = in_already_reconciled
     )
+    # Reformat the adjacencies file created by DeCoSTAR to rename genes, families and species
     decostar_reformat_adjacencies_file(
         species_map, genes_map, in_adjacencies_file,
         out_adjacencies_dir
diff --git a/scripts/DeCoSTAR_statistics.py b/scripts/DeCoSTAR_statistics.py
index 9cd4235..59d5567 100755
--- a/scripts/DeCoSTAR_statistics.py
+++ b/scripts/DeCoSTAR_statistics.py
@@ -5,14 +5,14 @@
 
 __author__    = "Cedric Chauve"
 __email__     = "cedric.chauve@sfu.ca"
-__version__   = "1.0"
+__version__   = "1.0.3"
 __status__    = "Released"
 
 import sys
 
 from data_utils import (
     data_species_list,
-    data_species2adjacencies_path
+    data_index2path
 )
 from DeCoSTAR_reformat import decostar_read_adjacencies
 
@@ -60,7 +60,7 @@ def decostar_read_results(in_genes_file, in_adjacencies_file, in_species_list):
     for (species,gene) in species_gene:
         adjacencies_dicts[species][gene] = {'h': [], 't': []}
     ## Populate dictionaries from species to adjacency tabulated file
-    species2adjacencies = data_species2adjacencies_path(in_adjacencies_file)
+    species2adjacencies = data_index2path(in_adjacencies_file)
     for species,in_adjacencies_file in species2adjacencies.items():
         in_adjacencies = decostar_read_adjacencies(
             in_adjacencies_file, species=species
diff --git a/scripts/GeneRax_create_input_files.py b/scripts/GeneRax_create_input_files.py
index 2fb8025..fab1c88 100755
--- a/scripts/GeneRax_create_input_files.py
+++ b/scripts/GeneRax_create_input_files.py
@@ -5,7 +5,7 @@
 
 __author__    = "Cedric Chauve"
 __email__     = "cedric.chauve@sfu.ca"
-__version__   = "1.0"
+__version__   = "1.0.3"
 __status__    = "Released"
 
 import sys
@@ -14,11 +14,11 @@
 from data_utils import (
     data_family2genes,
     data_gene2species,
-    data_family2alignment_path
+    data_index2path
 )
 
 ''' Write the GeneRax families file from paths to alignments '''
-def GeneRax_write_families_file(
+def generax_write_families_file(
         in_family2genes, in_gene2species, in_family2alignment,
         in_subst_model,
         out_map_files_dir, out_families_file
@@ -58,11 +58,9 @@ def main():
     # Read all genes
     gene2species = data_gene2species(in_gene_orders_file)
     # Read alignmed families
-    family2alignment = data_family2alignment_path(
-        in_alignments_file, in_suffix
-    )
+    family2alignment = data_index2path(in_alignments_file)
     # Create GeneRax input files
-    GeneRax_write_families_file(
+    generax_write_families_file(
         family2genes, gene2species, family2alignment, in_subst_model,
         out_map_files_dir, out_families_file
     )
diff --git a/scripts/GeneRax_reformat.py b/scripts/GeneRax_reformat.py
index 08bb320..0282015 100755
--- a/scripts/GeneRax_reformat.py
+++ b/scripts/GeneRax_reformat.py
@@ -5,7 +5,7 @@
 
 __author__    = "Cedric Chauve"
 __email__     = "cedric.chauve@sfu.ca"
-__version__   = "1.0"
+__version__   = "1.0.3"
 __status__    = "Released"
 
 import sys
@@ -13,51 +13,85 @@
 
 from recPhyloXML_utils import xml_reformat_file
 
-def get_families_from_input(in_GeneRax_families_file):
-    with open(in_GeneRax_families_file, 'r') as in_file:
-        families = [
+# Suffix of reconciliation files created by GeneRax
+GENERAX_XML_SUFFIX = '_reconciliated.xml'
+# Nam of a GeneRax gene tree in Newick format
+GENERAX_GT_NEWICK = 'geneTree.newick'
+
+''' Read families ID from a GeneRax families file '''
+def generax_get_families_from_input(in_generax_families_file):
+    '''
+    input: path to GeneRax families file
+    output: list of families ID
+    '''
+    with open(in_generax_families_file, 'r') as in_file:
+        generax_families = [
             f.rstrip()[2:]
             for f in in_file.readlines()
             if f.startswith('- ')
         ]
-    return families
+    return generax_families
 
-def reformat_reconciliations(families, results_dir, suffix):
+''' Reformat the recPhyloXML files created by GeneRax '''
+def generax_reformat_reconciliations(generax_families, results_dir, suffix):
+    '''
+    input: 
+    - list of GeneRax families ID
+    - directory containing GeneRax results
+    - suffix of refortmated reconciliations files
+    output:
+    - creates one reformatted file for every GeneRax reconciliation
+    - labels all ancestral genes by integers in increasing order (starting at 0)
+    '''
     current_gene_id = 0 # current gene number
-    for fam_id in families:
+    for fam_id in generax_families:
         in_file = os.path.join(
-            results_dir, 'reconciliations',
-            f'{fam_id}_reconciliated.xml'
+            results_dir, 'reconciliations', f'{fam_id}{GENERAX_XML_SUFFIX}'
         )
         out_file = os.path.join(
-            results_dir, 'reconciliations',
-        f'{fam_id}{suffix}'
+            results_dir, 'reconciliations', f'{fam_id}{suffix}'
         )
         if os.path.isfile(in_file):
             current_gene_id = xml_reformat_file(
-                in_file, out_file,
-                start_id=current_gene_id
+                in_file, out_file, start_id=current_gene_id
             )
 
-def create_gene_trees_file(families, results_dir, out_gene_trees_file):
+''' Creates a tabulated file <family ID><TA><GeneRax gene tree file path> '''
+def generax_create_gene_trees_file(generax_families, results_dir, out_gene_trees_file):
+    '''
+    input: 
+    - list of families ID
+    - directory containing GeneRax results
+    - tabulated file to create
+    output:
+    - creates out_gene_trees_file
+    '''
     with open(out_gene_trees_file, 'w') as out_file:
-        for fam_id in families:
-            in_file = os.path.join(
-                results_dir, 'results', fam_id,
-                'geneTree.newick'
+        for fam_id in generax_families:
+            gt_file = os.path.join(
+                results_dir, 'results', fam_id, GENERAX_GT_NEWICK
             )
-            if os.path.isfile(in_file):
-                out_file.write(f'{fam_id}\t{in_file}\n')
+            if os.path.isfile(gt_file):
+                out_file.write(f'{fam_id}\t{gt_file}\n')
 
 def main():
-    in_GeneRax_families_file = sys.argv[1]
+    in_generax_families_file = sys.argv[1]
     results_dir = sys.argv[2]
     rec_ext = sys.argv[3]
     out_gene_trees_file = sys.argv[4]
 
-    families = get_families_from_input(in_GeneRax_families_file)
-    reformat_reconciliations(families, results_dir, rec_ext)
-    create_gene_trees_file(families, results_dir, out_gene_trees_file)
+    # Read GeneRax families ID from GenRax families file
+    generax_families = generax_get_families_from_input(
+        in_generax_families_file
+    )
+    # Reformat GeneRax reconciliations files
+    generax_reformat_reconciliations(
+        generax_families, results_dir, rec_ext
+    )
+    # Creates a gene trees file from GeneRax gene trees
+    generax_create_gene_trees_file(
+        generax_families, results_dir, out_gene_trees_file
+    )
 
 if __name__ == "__main__":
     main()
diff --git a/scripts/SPPDCJ_create_input_files.py b/scripts/SPPDCJ_create_input_files.py
index 1d9578c..0d621e5 100755
--- a/scripts/SPPDCJ_create_input_files.py
+++ b/scripts/SPPDCJ_create_input_files.py
@@ -5,13 +5,13 @@
 
 __author__    = "Cedric Chauve"
 __email__     = "cedric.chauve@sfu.ca"
-__version__   = "0.99"
-__status__    = "Development"
+__version__   = "1.0.3"
+__status__    = "Released"
 
 import sys
 import ete3
 
-from data_utils import data_species2adjacencies_path
+from data_utils import data_index2path
 from newick_utils import (
     newick_get_children_map,
     newick_get_lca_species
@@ -63,7 +63,7 @@ def split_gene(gene):
     
     species2adjacencies_file = [
         (species,adj_path)
-        for (species,adj_path) in data_species2adjacencies_path(
+        for (species,adj_path) in data_index2path(
                 in_adjacencies_file
         ).items()
         if (species_list is None or species in species_list)
@@ -105,18 +105,20 @@ def main():
     out_species_tree = sys.argv[5]
     out_adjacencies_file = sys.argv[6]
 
-    if in_extant_species == 'all':
+    # Define species to consider
+    if in_extant_species == 'all':# Consider all species
         species_list = None
-    else:
+    else:# Consider species covered by the LCA of in_extant_species
         species_list = newick_get_lca_species(
             in_species_tree, in_extant_species.split()
         )
-    
+    # Creates an SPP-DCJ species tree
     sppdcj_species_trees(
         in_species_tree,
         out_species_tree,
         species_list=species_list
     )
+    # Creates an SPP-DCJ adjacencies file
     sppdcj_adjacencies(
         in_adjacencies_file, in_weight_threshold,
         out_adjacencies_file,
diff --git a/scripts/SPPDCJ_reformat.py b/scripts/SPPDCJ_reformat.py
index ac4b17d..ed1c1a9 100755
--- a/scripts/SPPDCJ_reformat.py
+++ b/scripts/SPPDCJ_reformat.py
@@ -5,13 +5,13 @@
 
 __author__    = "Cedric Chauve"
 __email__     = "cedric.chauve@sfu.ca"
-__version__   = "1.0"
+__version__   = "1.0.3"
 __status__    = "Released"
 
 import sys
 import os
 
-from data_utils import data_species2adjacencies_path
+from data_utils import data_index2path
 
 from DeCoSTAR_reformat import (
     decostar_sep,
@@ -21,7 +21,7 @@
 from DeCoSTAR_statistics import decostar_sign2extremity
 
 ''' Read the SPPDCJ adajcencies file and create a species-indexed dictionary '''
-def read_sppdcj_adjacencies(in_adjacencies_file):
+def sppdcj_read_sppdcj_adjacencies(in_adjacencies_file):
     '''
     input: SPPDCJ adjacencies file
     output: dict(species -> dict((gene1,ext1,gene2,ext2)->weight)
@@ -48,12 +48,12 @@ def read_sppdcj_adjacencies(in_adjacencies_file):
     return adjacencies_dict
 
 ''' Read the DeCoSTAR adajcencies file and create a species-indexed dictionary '''
-def read_decostar_adjacencies(in_data_adjacencies_file):
+def sppdcj_read_decostar_adjacencies(in_data_adjacencies_file):
     '''
     input: data adjacencies file (species<TAB>DeCoSTAR adjacencies file
     output: dict(species -> dict((gene1,ext1,gene2,ext2)->(gene1,sign1,gene2,sign2,weight1,weight2))
     '''
-    species2adjacencies_files = data_species2adjacencies_path(in_data_adjacencies_file)
+    species2adjacencies_files = data_index2path(in_data_adjacencies_file)
     species2adjacencies_aux = {}
     for species,adjacencies_file in species2adjacencies_files.items():
         species2adjacencies_aux[species] = decostar_read_adjacencies(adjacencies_file, species=species)
@@ -72,7 +72,7 @@ def read_decostar_adjacencies(in_data_adjacencies_file):
     return adjacencies_dict
 
 ''' Filter DeCoSTAR adjacencies discarded by SPPDCJ '''
-def filter_adjacencies(in_decostar_adjacencies, in_sppdcj_adjacencies):
+def sppdcj_filter_adjacencies(in_decostar_adjacencies, in_sppdcj_adjacencies):
     '''
     input: dictionaries
     dict(species -> dict((gene1,gene2,ext1,ext2)->weight)
@@ -90,7 +90,7 @@ def filter_adjacencies(in_decostar_adjacencies, in_sppdcj_adjacencies):
     return out_adjacencies
 
 ''' Write the filtered adjacncies '''
-def write_adjacencies(adjacencies_dict,out_dir):
+def sppdcj_write_adjacencies(adjacencies_dict,out_dir):
     for species,adjacencies_dict in adjacencies_dict.items():
         out_adjacencies_path = os.path.join(out_dir, f'{species}_adjacencies.txt')
         with open(out_adjacencies_path,'w') as out_adjacencies_file:
@@ -102,13 +102,20 @@ def main():
     in_data_adjacencies_file = sys.argv[1]
     in_sppdcj_adjacencies_file = sys.argv[2]
     out_dir = sys.argv[3]
+    
     # Reading SPPDCJ adjacencies
-    sppdcj_adjacencies = read_sppdcj_adjacencies(in_sppdcj_adjacencies_file)    
+    sppdcj_adjacencies = sppdcj_read_sppdcj_adjacencies(
+        in_sppdcj_adjacencies_file
+    )    
     # Reading DeCoSTAR adjacencies
-    decostar_adjacencies = read_decostar_adjacencies(in_data_adjacencies_file)
+    decostar_adjacencies = sppdcj_read_decostar_adjacencies(
+        in_data_adjacencies_file
+    )
     # Filter DeCoSTAR adjacencies
-    filtered_adjacencies = filter_adjacencies(decostar_adjacencies,sppdcj_adjacencies)
-    write_adjacencies(filtered_adjacencies,out_dir)
+    filtered_adjacencies = sppdcj_filter_adjacencies(
+        decostar_adjacencies,sppdcj_adjacencies
+    )
+    sppdcj_write_adjacencies(filtered_adjacencies,out_dir)
 
 if __name__ == "__main__":
     main()
diff --git a/scripts/SPPDCJ_statistics.py b/scripts/SPPDCJ_statistics.py
index 36fbeb3..e5c0061 100755
--- a/scripts/SPPDCJ_statistics.py
+++ b/scripts/SPPDCJ_statistics.py
@@ -5,19 +5,19 @@
 
 __author__    = "Cedric Chauve"
 __email__     = "cedric.chauve@sfu.ca"
-__version__   = "1.0"
+__version__   = "1.0.3"
 __status__    = "Released"
 
 import sys
 import os
 
 from SPPDCJ_reformat import (
-    read_sppdcj_adjacencies,
-    read_decostar_adjacencies,
-    filter_adjacencies
+    sppdcj_read_sppdcj_adjacencies,
+    sppdcj_read_decostar_adjacencies,
+    sppdcj_filter_adjacencies
 )
 
-def SPPDCJ_statistics(decostar_adjacencies, filtered_adjacencies):
+def sppdcj_statistics(decostar_adjacencies, filtered_adjacencies):
     statistics = {}
     for species,adjacencies in decostar_adjacencies.items():
         statistics[species] = {}
@@ -32,7 +32,7 @@ def SPPDCJ_statistics(decostar_adjacencies, filtered_adjacencies):
         statistics[species]['weight2'] = sum_weights
     return statistics
 
-def write_statistics(statistics, out_statistics_file):
+def sppdcj_write_statistics(statistics, out_statistics_file):
     with open(out_statistics_file,'w') as out_file:
         out_file.write('#species\tnumber of adjacencies:total weight:kept adjacencies:kept weight')
         for species,stats in statistics.items():
@@ -45,14 +45,14 @@ def main():
     in_sppdcj_adjacencies_file = sys.argv[2]
     out_statistics_file = sys.argv[3]
     # Reading SPPDCJ adjacencies
-    sppdcj_adjacencies = read_sppdcj_adjacencies(in_sppdcj_adjacencies_file)    
+    sppdcj_adjacencies = sppdcj_read_sppdcj_adjacencies(in_sppdcj_adjacencies_file)    
     # Reading DeCoSTAR adjacencies
-    decostar_adjacencies = read_decostar_adjacencies(in_data_adjacencies_file)
+    decostar_adjacencies = sppdcj_read_decostar_adjacencies(in_data_adjacencies_file)
     # Filter DeCoSTAR adjacencies
-    filtered_adjacencies = filter_adjacencies(decostar_adjacencies,sppdcj_adjacencies)
+    filtered_adjacencies = sppdcj_filter_adjacencies(decostar_adjacencies,sppdcj_adjacencies)
     # Statistics
-    statistics = SPPDCJ_statistics(decostar_adjacencies, filtered_adjacencies)
-    write_statistics(statistics, out_statistics_file)
+    statistics = sppdcj_statistics(decostar_adjacencies, filtered_adjacencies)
+    sppdcj_write_statistics(statistics, out_statistics_file)
 
 if __name__ == "__main__":
     main()
diff --git a/scripts/data_utils.py b/scripts/data_utils.py
index 1731188..0219840 100644
--- a/scripts/data_utils.py
+++ b/scripts/data_utils.py
@@ -5,7 +5,7 @@
 
 __author__    = "Cedric Chauve"
 __email__     = "cedric.chauve@sfu.ca"
-__version__   = "1.0"
+__version__   = "1.0.3"
 __status__    = "Released"
 
 import sys
@@ -87,68 +87,14 @@ def data_family2genes(in_families_file):
     output: dict(family ID -> list(genes))
     '''
     return _data_create_map(in_families_file, sep2=' ')
-    
-''' Creates a map from species to gene order file '''
-def data_species2gene_order_path(in_gene_orders_file):
-    '''
-    input: path to dataset gene orders file
-    output: dict(species -> gene order file path)
-    '''
-    return _data_create_map(in_gene_orders_file)
-
-''' Creates a map from species to adjacencies file '''
-def data_species2adjacencies_path(in_adjacencies_file):
-    '''
-    input: path to dataset gene orders file
-    output: dict(species -> adjacencies file path)
-    '''
-    return _data_create_map(in_adjacencies_file)
 
-''' Creates a map from family to sequences file '''
-def data_family2sequences_path(in_sequences_file):
-    '''
-    input: path to dataset sequences file
-    output: dict(family -> sequences path)
-    '''
-    return _data_create_map(in_reconciliations_file)
+''' Creates a map from index to files path '''
+def data_index2path(in_file):
+    return _data_create_map(in_file)
 
-''' Creates a map from family to alignment file '''
-def data_family2alignment_path(in_alignments_file, in_suffix):
-    '''
-    input: path to dataset alignments file
-    output: dict(family -> alignment path) if path ends by in_suffix
-    '''
-    family2alignment_path = {}
-    with open(in_alignments_file, 'r') as alignments:
-        for family in alignments.readlines():
-            fam_id,alignment_file = family.rstrip().split('\t')
-            if alignment_file.endswith(in_suffix):
-                family2alignment_path[fam_id] = alignment_file
-    return family2alignment_path
-
-''' Creates a map from family to gene tree(s) file '''
-def data_family2genetree_path(in_gene_trees_file):
-    '''
-    input: path to dataset gene trees file
-    output: dict(family -> gene tree(s) path)
-    '''
-    return _data_create_map(in_gene_trees_file)
-
-''' Creates a map from family to reconciliation file '''
-def data_family2reconciliation_path(in_reconciliations_file):
-    '''
-    input: path to dataset reconciliations file
-    output: dict(family -> reconciliation path)
-    '''
-    return _data_create_map(in_reconciliations_file)
-
-''' Creates a map from reconciliation file to family '''
-def data_reconciliation_path2family(in_reconciliations_file):
-    '''
-    input: path to dataset reconciliations file
-    output: dict(family -> reconciliation path)
-    '''
-    return _data_create_inverse_map(in_reconciliations_file)
+''' Creates a map from files path to index '''
+def data_path2index(in_file):
+    return _data_create_inverse_map(in_file)
 
 ''' Creates a list of species '''
 def data_species_list(in_file):
@@ -324,7 +270,7 @@ def data_check_gene_orders_file(in_gene_orders_file, species_list, genes_list):
     - genes errors:    3,[list of genes in gene orders files not in genes list,list of genes in genes list not in gene orders files]
     - missing files:   4,[missing files]
     '''
-    species2gene_order_path = data_species2gene_order_path(in_gene_orders_file)
+    species2gene_order_path = data_index2path(in_gene_orders_file)
     go_species_list = species2gene_order_path.keys()
     # Checking species lists
     species_diff = _data_compare_lists(go_species_list,species_list)
diff --git a/scripts/fasta_utils.py b/scripts/fasta_utils.py
index 509eaaa..287b711 100644
--- a/scripts/fasta_utils.py
+++ b/scripts/fasta_utils.py
@@ -5,7 +5,7 @@
 
 __author__    = "Cedric Chauve"
 __email__     = "cedric.chauve@sfu.ca"
-__version__   = "1.0"
+__version__   = "1.0.3"
 __status__    = "Released"
 
 import sys
diff --git a/scripts/gene_orders_utils.py b/scripts/gene_orders_utils.py
index 99a7060..602b85c 100755
--- a/scripts/gene_orders_utils.py
+++ b/scripts/gene_orders_utils.py
@@ -5,7 +5,7 @@
 
 __author__    = "Cedric Chauve"
 __email__     = "cedric.chauve@sfu.ca"
-__version__   = "1.0"
+__version__   = "1.0.3"
 __status__    = "Released"
 
 import os
@@ -13,12 +13,14 @@
 from collections import defaultdict
 import networkx as nx
 
-from data_utils import data_species2adjacencies_path
+from data_utils import data_index2path
 from DeCoSTAR_reformat import decostar_sep
 from DeCoSTAR_statistics import decostar_sign2extremity
 
+""" Reading input data to create CARs: DeCoSTAR-format genes and adjacencies """
+
 ''' Read DeCoSTAR genes for all species '''
-def read_DeCoSTAR_genes(in_genes_file):
+def go_read_decostar_genes(in_genes_file):
     '''
     input: DeCoSTAR genes file, for all species
     output: dict(species -> list of genes in format family<decostar_sep>gene)
@@ -32,7 +34,7 @@ def read_DeCoSTAR_genes(in_genes_file):
     return genes_dict
 
 ''' Read adjacencies for a given species '''
-def read_DeCoSTAR_adjacencies_species(in_adjacencies_file):
+def go_read_decostar_adjacencies_species(in_adjacencies_file):
     '''
     input: DeCoSTAR adjacencies file, for one species
     output: list((gene1,sign1,gene2,sign2,weight))
@@ -44,23 +46,33 @@ def read_DeCoSTAR_adjacencies_species(in_adjacencies_file):
             gene1,sign1 = adjacency_data[0],adjacency_data[2]
             gene2,sign2 = adjacency_data[1],adjacency_data[3]
             weight = adjacency_data[5]
-            adjacencies_list.append((gene1,gene2,sign1,sign2,weight))
+            adjacencies_list.append(
+                (gene1,gene2,sign1,sign2,weight)
+            )
     return adjacencies_list
 
 ''' Read adjacencies for all species '''
-def read_DeCoSTAR_adjacencies(in_adjacencies_file):
+def go_read_decostar_adjacencies(in_adjacencies_file):
     '''
     input: adjacencies file
     output: dict(species -> list((gene1,sign1,gene2,sign2,weight)))
     '''
     adjacencies_dict = {}
-    species2adjacencies_file = data_species2adjacencies_path(in_adjacencies_file)
+    species2adjacencies_file = data_index2path(in_adjacencies_file)
     for species,adjacencies_file_path in species2adjacencies_file.items():
-        adjacencies_dict[species] = read_DeCoSTAR_adjacencies_species(adjacencies_file_path)
+        adjacencies_dict[species] = go_read_decostar_adjacencies_species(
+            adjacencies_file_path
+        )
     return adjacencies_dict
 
-''' Create a graph from genes and adjacencies '''
-def create_adjacencies_graph(in_genes_list, in_adjacencies):
+""" Graph creation and manipulation """
+
+''' 
+Create graphs from genes and adjacencies, on per species
+Vertices = gene extremities
+Edges = adjacencies, each with a weight
+'''
+def go_create_adjacencies_graph(in_genes_list, in_adjacencies):
     '''
     input:
     - dict(species -> list of genes list(family<decostar_sep>gene))
@@ -76,56 +88,80 @@ def create_adjacencies_graph(in_genes_list, in_adjacencies):
             graphs[species].add_edge((gene,'h'),(gene,'t'),weight=0)
         for (gene1,gene2,sign1,sign2,weight) in in_adjacencies_list:
             exts = decostar_sign2extremity[(sign1,sign2)]
-            graphs[species].add_edge((gene1,exts[0]),(gene2,exts[1]), weight=weight)
+            graphs[species].add_edge(
+                (gene1,exts[0]),(gene2,exts[1]),
+                weight=weight
+            )
     return graphs
 
-''' Graph to FASTA string '''
-
-def check_linear(C):
-    ''' Check if a component is linear '''
+def go_check_linear(C):
+    ''' Check if a component C (networkx graph) is linear '''
     return C.number_of_nodes() == C.number_of_edges()+1
 
-def get_start_node(C):
-    ''' Return the first node for a traversal of a component '''
+def go_get_start_node(C):
+    ''' Return the first node for a traversal of a component C '''
     nodes = list(C.nodes)
-    if check_linear(C):
+    if go_check_linear(C):
         return [x for x in nodes if C.degree(x)==1][0]
     else:
         return nodes[0]
 
-def signed_gene(edge):
+def go_signed_gene(edge):
+    ''' 
+    Add a "-" before a the gene defined by the first gene extremity 
+    of an edge if this extremity is a tail 
+    '''
     if edge[0][1] == 't':
         return f'{edge[0][0]}'
     else:
         return f'-{edge[0][0]}'
+
+
+''' Graph to CARs in FASTA-like format '''
     
-def traversal2FASTA(C, start_node, species, C_id):
-    ''' DFS traversal of a component '''
+def go_component2str(C, start_node, species, C_id):
+    ''' 
+    DFS traversal of a component C (assumed to be linear or circular)
+    given the first node for the traversal and the ID of the 
+    component.
+    species is needed to remove the gene name
+    Creates a FASTA-like string describing the oriented gene order
+    of the traversal
+    '''
     edges_list = list(nx.dfs_edges(C, source=start_node))
-    nodes_list = [signed_gene(edge).replace(f'{species}|','') for edge in edges_list if edge[0][0]==edge[1][0]]
+    nodes_list = [
+        go_signed_gene(edge).replace(f'{species}|','')
+        for edge in edges_list
+        if edge[0][0]==edge[1][0]
+    ]
     nodes_str = ' '.join(nodes_list)
     C_str = f'>{C_id}\n{nodes_str}\n'
     return C_str
     
-def graph2FASTA(in_graph, species):
+def go_graph2str(in_graph, species):
     '''
     input: graph, species
-    output: FASTA str
+    output: string in FASTA-like format for all components of the graph
     '''
     components = list(nx.connected_components(in_graph))
     component_id = 1
-    FASTA_str = ''
+    result = ''
     for component in components:
-        subgraph = nx.induced_subgraph(in_graph, component)
-        start_node = get_start_node(subgraph)
-        FASTA_str += traversal2FASTA(subgraph, start_node, species, component_id)
+        C = nx.induced_subgraph(in_graph, component)
+        start_node = go_get_start_node(C)
+        result += go_component2str(
+            C, start_node, species, component_id
+        )
         component_id += 1
-    return FASTA_str
+    return result
 
-def write_FASTA(in_graphs, out_dir, out_file_path):
+def go_write_CARs(in_graphs, out_dir, out_file_path):
+    '''
+    Write CARs
+    '''
     with open(out_file_path,'w') as out_data_file:
         for species,graph in in_graphs.items():
-            species_str = graph2FASTA(graph,species)
+            species_str = go_graph2str(graph,species)
             species_out_file = os.path.join(out_dir,f'{species}_CARs.txt')
             out_data_file.write(f'{species}\t{species_out_file}\n')
             with open(species_out_file,'w') as out_file:
@@ -133,12 +169,10 @@ def write_FASTA(in_graphs, out_dir, out_file_path):
 
 ''' Statistics about a graph '''
 
-def graph2stats(in_graph):
+def go_graph2stats(in_graph):
     '''
-    input: graph, species
-    output: 
-    - dict(nb_nodes -> dict(nb_edges -> number of components))
-    
+    input: graph
+    output:  dict(nb_nodes -> dict(nb_edges -> number of components))    
     '''
     components = list(nx.connected_components(in_graph))
     components_stats = defaultdict(lambda: defaultdict(int))
@@ -151,7 +185,7 @@ def graph2stats(in_graph):
         components_stats[nb_genes][nb_adjacencies] += 1
     return components_stats
 
-def write_stats(in_stats, out_file_path):
+def go_write_stats(in_stats, out_file_path):
     '''
     input: dict(species -> dict(nb_nodes -> dict(nb_edges -> number of components)), stats file
     '''
@@ -178,20 +212,22 @@ def main():
     in_data_adjacencies_file = sys.argv[3]
     out_dir = sys.argv[4]
     out_file = sys.argv[5]
-    # Reading genes
-    genes = read_DeCoSTAR_genes(in_genes_file)
+    
+    # Reading DeCoSTAR genes
+    genes = go_read_decostar_genes(in_genes_file)
     # Reading DeCoSTAR adjacencies
-    adjacencies = read_DeCoSTAR_adjacencies(in_data_adjacencies_file)
+    adjacencies = go_read_decostar_adjacencies(in_data_adjacencies_file)
     # Create graphs
-    graphs = create_adjacencies_graph(genes, adjacencies)
+    graphs = go_create_adjacencies_graph(genes, adjacencies)
     if command == 'build':
-        # Read graphs and write into FASTA
-        write_FASTA(graphs, out_dir, out_file)
+        # Read graphs and write CARs
+        go_write_CARs(graphs, out_dir, out_file)
     elif command == 'stats':
+        # Compute and write statistics
         species_stats = {}
         for species,graph in graphs.items():
-            species_stats[species] = graph2stats(graphs[species])
-        write_stats(species_stats, out_file)
+            species_stats[species] = go_graph2stats(graphs[species])
+        go_write_stats(species_stats, out_file)
             
 if __name__ == "__main__":
     main()
diff --git a/scripts/newick_utils.py b/scripts/newick_utils.py
index e6c4585..b52de04 100755
--- a/scripts/newick_utils.py
+++ b/scripts/newick_utils.py
@@ -5,16 +5,13 @@
 
 __author__    = "Cedric Chauve"
 __email__     = "cedric.chauve@sfu.ca"
-__version__   = "1.0"
+__version__   = "1.0.3"
 __status__    = "Released"
 
 import sys
 from collections import defaultdict
 import ete3
 
-NEWICK_EXTANT='extant'
-NEWICK_ANCESTRAL='ancestral'
-
 ''' Check that the tree is rooted '''
 def newick_check_rooted(species_tree_file):
     '''
@@ -95,21 +92,6 @@ def newick_remove_internal_names(in_species_tree_file, out_species_tree_file):
     tree = ete3.Tree(in_species_tree_file, format=1)
     tree.write(format=5, outfile=out_species_tree_file)
 
-''' Creates a map from species names to species status '''
-def newick_get_species_status(tree_file):
-    '''
-    input: paths to a Newick tree file with internal nodes named
-    output: dic(str->str) node (species) name -> 'extant', 'ancestral'
-    '''
-    species = {}
-    tree = ete3.Tree(tree_file, format=1)
-    for node in tree.traverse():
-        if node.is_leaf():
-            species[node.name] = NEWICK_EXTANT
-        else:
-            species[node.name] = NEWICK_ANCESTRAL
-    return(species)
-
 ''' Creates a map from node names to children '''
 def newick_get_children_map(tree_file):
     '''
@@ -164,10 +146,12 @@ def main():
     command = sys.argv[1]
 
     if command == 'species':
+        # Creates a species -> descendants file from a species tree
         in_species_tree_file = sys.argv[2]
         out_species_file = sys.argv[3]
         newick_create_species_file(in_species_tree_file, out_species_file)
     elif command == 'unlabel':
+        # Creates a new file with internal nodes unlabeled
         in_species_tree_file = sys.argv[2]
         out_species_tree_file = sys.argv[3]
         newick_remove_internal_names(in_species_tree_file, out_species_tree_file)
diff --git a/scripts/recPhyloXML_statistics.py b/scripts/recPhyloXML_statistics.py
index b1d6d8c..1ef9d6a 100755
--- a/scripts/recPhyloXML_statistics.py
+++ b/scripts/recPhyloXML_statistics.py
@@ -5,12 +5,12 @@
 
 __author__    = "Cedric Chauve"
 __email__     = "cedric.chauve@sfu.ca"
-__version__   = "1.0"
+__version__   = "1.0.3"
 __status__    = "Released"
 
 import sys
 
-from data_utils import data_family2reconciliation_path
+from data_utils import data_index2path
 from recPhyloXML_utils import (
     xml_get_tag,
     xml_get_prefix,
@@ -64,7 +64,7 @@ def parse_clade_recursive(node, result):
     parse_clade_recursive(root, result)
     return result
 
-def recPhyloXML_read_events(in_file):
+def xml_read_events(in_file):
     ''' 
     Read a recPhyloXML file and returns a dictionary indexed by species
     and for each containing a dictionary recording number of genes, 
@@ -118,20 +118,20 @@ def parse_clade_recursive(node, tag_pref, stats):
 
 
 ''' Collects statistics from a dataset reconciliations file '''
-def collect_statistics(in_reconciliations_file):
+def xml_collect_statistics(in_reconciliations_file):
     '''
     input: dataset path family ID -> path to reconciliation file
     output:
     - dict(species -> dict(key: value for key in STATS_keys))
     - dict(family ID -> dict(species -> dict(key: value for key in STATS_keys)))
     '''
-    family2reconciliation = data_family2reconciliation_path(
+    family2reconciliation = data_index2path(
         in_reconciliations_file
     )
     stats_species = {}
     stats_families = {}
     for fam_id,reconciliation_path in family2reconciliation.items():  
-        events = recPhyloXML_read_events(reconciliation_path)
+        events = xml_read_events(reconciliation_path)
         stats_families[fam_id] = events
         for species,stats in stats_families[fam_id].items():
             if species not in stats_species.keys():
@@ -151,7 +151,7 @@ def _stats_str(stats, sp, sep=':'):
         ]
     )
 
-def write_statistics_species(
+def xml_write_statistics_species(
         in_statistics_species,
         out_stats_file_species,
         sep1=':', sep2='\t', sep3=' '
@@ -165,7 +165,7 @@ def write_statistics_species(
             )
         out_stats_file.write('\n')
 
-def write_statistics_families(
+def xml_write_statistics_families(
         in_statistics_families,
         out_stats_file_families,
         sep1=':', sep2='\t', sep3=' '
@@ -199,15 +199,15 @@ def main():
     out_stats_file_families = sys.argv[3]
 
     # Reading reconciliations and collecting statistics
-    (statistics_families,statistics_species) = collect_statistics(
+    (statistics_families,statistics_species) = xml_collect_statistics(
         in_reconciliations_file
     )
     # Writting species statistics
-    write_statistics_species(
+    xml_write_statistics_species(
         statistics_species, out_stats_file_species
     )
     # Writting families statistics
-    write_statistics_families(
+    xml_write_statistics_families(
         statistics_families, out_stats_file_families
     )
 
diff --git a/scripts/recPhyloXML_utils.py b/scripts/recPhyloXML_utils.py
index b68d2f7..5a5aae6 100644
--- a/scripts/recPhyloXML_utils.py
+++ b/scripts/recPhyloXML_utils.py
@@ -5,7 +5,7 @@
 
 __author__    = "Cedric Chauve"
 __email__     = "cedric.chauve@sfu.ca"
-__version__   = "1.0"
+__version__   = "1.0.3"
 __status__    = "Released"
 
 import sys
diff --git a/src/AGO.py b/src/AGO.py
index 7665e15..5cf3110 100644
--- a/src/AGO.py
+++ b/src/AGO.py
@@ -5,7 +5,7 @@
 
 __author__    = "Cedric Chauve"
 __email__     = "cedric.chauve@sfu.ca"
-__version__   = "1.0"
+__version__   = "1.0.3"
 __status__    = "Released"
 
 import sys
diff --git a/src/AGO_parameters.py b/src/AGO_parameters.py
index c3e5a04..3a7d0f2 100644
--- a/src/AGO_parameters.py
+++ b/src/AGO_parameters.py
@@ -5,7 +5,7 @@
 
 __author__    = "Cedric Chauve"
 __email__     = "cedric.chauve@sfu.ca"
-__version__   = "1.0"
+__version__   = "1.0.3"
 __status__    = "Released"
 
 import sys
diff --git a/src/AGO_utils.py b/src/AGO_utils.py
index cc4205a..8bf19fc 100644
--- a/src/AGO_utils.py
+++ b/src/AGO_utils.py
@@ -5,7 +5,7 @@
 
 __author__    = "Cedric Chauve"
 __email__     = "cedric.chauve@sfu.ca"
-__version__   = "1.0"
+__version__   = "1.0.3"
 __status__    = "Released"
 
 import os
@@ -69,7 +69,7 @@ def create_bash_script(parameters, tool):
         script.write('#!/bin/bash\n\n')
         bash_modules = parameters.get_slurm_modules(tool)
         if bash_modules is not None:
-            script.write(f'\n\nmodule load {bash_modules}')        
+            script.write(f'\n\nmodule load {bash_modules}\n\n')        
         if parameters.check_slurm_array_input(tool):
             TASK_ID = '${TASK_ID}'
             array_size = parameters.get_slurm_array_input_len(tool)