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1. CAFE5-Gene-Family-Evolution-from-OrthoFinder-Results CAFE5-Gene-Family-Evolution-from-OrthoFinder-Results Public

   A set of scripts for running a CAFE5 gene family evolution analysis, from OrthoFinder's output.

   Shell

2. GO-Term-Enrichment-Analysis GO-Term-Enrichment-Analysis Public

   A Python script for testing over- and under-representation of Gene Ontology (GO) terms in a target gene set relative to a background set, using the hypergeometric test with Benjamini-Hochberg FDR c…

   Python

3. MSA-to-GeneRax MSA-to-GeneRax Public

   A workflow for gene family tree inference using GeneRax, from multiple sequence alignments.

   Shell

4. SC-Otho-to-RAxML SC-Otho-to-RAxML Public

   A pipeline to reconstruct a species tree with RaxML, from Single-Copy Orthologues (SCOs) identified by OrthoFinder.

   Shell

5. Phylogenomics-BUSCO-Analysis Phylogenomics-BUSCO-Analysis Public

   Forked from marievang/Phylogenomics-BUSCO-Analysis

   A phylogenomics workflow for processing BUSCO sequences, inferring gene trees, and reconstructing species trees using wASTRAL.

   Shell

6. GFF3-GO-Term-Extractor GFF3-GO-Term-Extractor Public

   A Perl utility for extracting Gene Ontology (GO) annotations from GFF3 annotation files.

   Perl