PlantTribes: A Collection of Automated Plant Gene Family Analysis Pipelines

PlantTribes is a collection of automated modular analysis pipelines that utilize objective classifications of complete protein sequences from sequenced plant genomes to perform evolutionary studies. It post-processes de novo assembly transcripts into putative coding sequences and their corresponding amino acid translations, estimates paralogous/orthologous pairwise synonymous/non-synonymous substitution rates for a set of gene sequences, classifies gene sequences into pre-computed orthologous plant gene family clusters, and builds gene family multiple sequence alignments and their corresponding phylogenies. A user provides de novo assembly transcripts, and PlantTribes produces predicted coding sequences and their corresponding translations, a table of pairwise synonymous/non-synonymous substitution rates for reciprocal best blast transcript pairs, results of significant duplication components in the distribution of Ks (synonymous substitutions) values, a summary table for transcripts classified into orthologous plant gene family clusters with their corresponding functional annotations, gene family amino acid and nucleotide fasta sequences, multiple sequence alignments, and inferred maximum likelihood phylogenies. Optionally, a user can provide externally predicted coding sequences and their corresponding amino acid translations derived from a transcriptome assembly or gene predictions from a sequenced genome. PlantTribes is freely available at https://github.com/dePamphilis/PlantTribes.