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Gene Family Analysis Pipeline: From Filtering to Orthologs Inference

A comprehensive pipeline for gene family analysis, starting with low-complexity masking and splices selection, through alignment and alignment masking, to orthologs inference. Includes bootstrapping, tree construction, and genetic distance calculations. Outputs orthologs predictions in text and NHX formats.

caleb-mcfadden
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Gene Family Analysis Pipeline: From Filtering to Orthologs Inference

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  1. Input: Gene Family (Multi-fasta file) Low-complexity masking CAST Splices selection SS* FILTERING Filtering procedure LEON* Gene id indexing GI* Filtered Gene family (Multi-fasta file) Alignment MAFFT Alignment refinement Rascal MULTIALIGNEMENT Alignment masking AL2CO Gene Family Alignement (PHYLIP Alignement) Bootstrapping alignement (x100) SeqBoot TREE CONSTRUCTION Genetic distance (x100) ProtDist Tree construction (x100) PHYML Rooting tree (x100) SDI Bootstrapped rooted trees (NHX) & genetic distances Set Bootstrap values on PHYML tree SB* ORTHOLOGS INFERENCE Gene id indexing GI* Orthologs Inference DoRIO Output: Orthologs predictions (.txt & NHX files)

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