Resources and tools

Github

Official repository from Gabaldon Lab.

Website

PhylomeDB

PhylomeDB is a public database for complete collections of gene phylogenies (phylomes). It allows users to interactively explore the evolutionary history of genes through the visualization of phylogenetic trees and multiple sequence alignments. Moreover, phylomeDB provides genome-wide orthology and paralogy predictions based on the analysis of the phylogenetic trees.

Website

MetaPhOrs

MetaPhOrs is a public repository of phylogeny-based orthology and paralogy predictions for most species with fully-sequenced genomes.

Website

Redundans

Redundans is a pipeline that assists an assembly of heterozygous/polymorphic genomes. Program takes as input assembled contigs, sequencing libraries and/or reference sequence and returns scaffolded homozygous genome assembly.

Website

ETE

ETE (Environment for Tree Exploration) is a python programming toolkit that assists in the automated manipulation, analysis and visualization of hierarchical trees. Supports large tree data structures, node annotation, independent editing and analysis of tree partitions, and the association of trees with external data such as multiple sequence alignments or numerical matrices.

Website

trimAl

trimAl is a tool for the automated removal of spurious sequences or poorly aligned regions from a multiple sequence alignment It also includes readAl, a format converter between most alignment formats.

Website