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Update CITATION_NOTICE
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raufs authored Aug 2, 2024
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Expand Up @@ -7,7 +7,7 @@ lsaBGC-Pan is made possible by many other tools including:

- Ortholog group identification:
- OrthoFinder2: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1832-y
- Panaroo:
- Panaroo: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-02090-4

- General processing of sequencing data and phylogenies:
- biopython: https://academic.oup.com/bioinformatics/article/25/11/1422/330687
Expand All @@ -25,17 +25,16 @@ lsaBGC-Pan is made possible by many other tools including:
- iTol: https://pubmed.ncbi.nlm.nih.gov/30931475/

- eGCF clustering and population-genetics analysis:
- zol:
- zol: https://www.biorxiv.org/content/10.1101/2023.06.07.544063v2
- DIAMOND: https://www.nature.com/articles/nmeth.3176
- MUSCLE5:
- MUSCLE5: https://www.nature.com/articles/s41467-022-34630-w

- Orthogroup to orthogroup and GCF to GCF (dis-)association analysis:
- pyseer:
- pyseer: https://academic.oup.com/bioinformatics/article/34/24/4310/5047751

- Annotation databases (from zol):
- KOfam HMMs: https://academic.oup.com/bioinformatics/article/36/7/2251/5631907
- PGAP HMMs: https://pubmed.ncbi.nlm.nih.gov/27342282/
- MIBiG DB: https://academic.oup.com/nar/article/51/D1/D603/6833236
- Pfam DB:
- VOG DB:
- ISFinder DB:
- Pfam DB: https://academic.oup.com/nar/article/49/D1/D412/5943818?login=false
- ISFinder DB: https://academic.oup.com/nar/article/34/suppl_1/D32/1132247?login=false

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