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

Evolcust

Evolcust retrieves groups of genes that are conserved in terms of gene order across different species. The prediction is first performed pairwise but then predicted clusters are grouped into families of homologous clusters.

Website

Crossmapper

Crossmapper is an automated bioinformatics pipeline for asessing the rate of read crossmapping when two or more organisms are sequenced as one sample. The software can be used for planning such kind of experimental setups as dual- or multiple RNA-seq (mainly for host-pathogen, symbiont and cohabitant interaction studies), metagenomics studies, sequencing and analysis of hybrid species, allele-specific expression studies, and can be extended for the use in large sequencing facilities for resource optimization.

Github

Haplotypo

HaploTypo is a pipeline suited to map variants into haplotypes in genetic variation analyses. After mapping and variant calling on a phased reference genome, HaploTypo infers the haplotype correspondence for each heterozygous variant. It also generates two independent FASTA files for each reconstructed haplotype.

Github