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lines changed Original file line number Diff line number Diff line change @@ -7,7 +7,7 @@ lsaBGC-Pan is made possible by many other tools including:
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- Ortholog group identification:
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- OrthoFinder2: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1832-y
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- - Panaroo:
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+ - Panaroo: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-02090-4
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- General processing of sequencing data and phylogenies:
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- biopython: https://academic.oup.com/bioinformatics/article/25/11/1422/330687
@@ -25,17 +25,16 @@ lsaBGC-Pan is made possible by many other tools including:
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- iTol: https://pubmed.ncbi.nlm.nih.gov/30931475/
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- eGCF clustering and population-genetics analysis:
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- - zol:
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+ - zol: https://www.biorxiv.org/content/10.1101/2023.06.07.544063v2
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- DIAMOND: https://www.nature.com/articles/nmeth.3176
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- - MUSCLE5:
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+ - MUSCLE5: https://www.nature.com/articles/s41467-022-34630-w
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- Orthogroup to orthogroup and GCF to GCF (dis-)association analysis:
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- - pyseer:
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+ - pyseer: https://academic.oup.com/bioinformatics/article/34/24/4310/5047751
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- Annotation databases (from zol):
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- KOfam HMMs: https://academic.oup.com/bioinformatics/article/36/7/2251/5631907
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- PGAP HMMs: https://pubmed.ncbi.nlm.nih.gov/27342282/
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- MIBiG DB: https://academic.oup.com/nar/article/51/D1/D603/6833236
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- - Pfam DB:
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- - VOG DB:
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- - ISFinder DB:
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+ - Pfam DB: https://academic.oup.com/nar/article/49/D1/D412/5943818?login=false
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+ - ISFinder DB: https://academic.oup.com/nar/article/34/suppl_1/D32/1132247?login=false
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