A pipeline to select optimal markers for microbial phylogenomics and species tree estimation using the multispecies coalescent and concatenation approaches

rapid phylogenomic tree calculator - A highly customizable framework for reproducible phylogenomic inference

Bash scripts for analysis of Hyb-Seq data (from raw reads to species trees)

Sondovač is a script to create orthologous low-copy nuclear probes from transcriptome and genome skim data for target enrichment. For latest version check "releases".

Genomic Epidemiology of SARS-CoV-2 in Pakistan

Call core SNPs agains a reference genome for a set of bacterial isolates, and build a phylogenetic tree based on the core-genome SNP information.

This pipeline helps to build a phylogenetic tree using the BUSCO results over a group of species/genomes/proteomes/transcriptomes.

🌱 📋 ➡️ 🎱 ➡️ 🌴 🌲 🌳 - A quick phylogenetic tree building pipeline!

Detect Hepatitis A Virus Infection Clusters

phylogenomics analysis for arabidopsis maf-cap genes

Mutual Information Supermatrix Phylogenomics Pipeline (MISPhyl): Reconstructs Phylogenomics Tree based on Mutual Information Evaluated Phylogenetics Signals From Genomes Derived Orthologous Sets

a bash based evolautionary pangenome analysis

This repository includes scripts and data used in Sgarlata et al., 2023 entitled "The Genomic Diversity of the Eliurus genus in northern Madagascar with a Putative New Species".

analyzing bacterial genome based ontologies and phylogenomics informativeness