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/networks)

ML phylogenetic inference for non-model organisms with short reads & assemblies

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".

Reproducible phylogenomics pipeline that builds partitioned species trees from BUSCO v5 results.

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.

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

Detect Hepatitis A Virus Infection Clusters

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

phylogenomics analysis for arabidopsis maf-cap genes

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".