All Published Workflows
15 workflows that have been reviewed and published
This is a phylogeny workflow for batch submission to HPC cluster built with Slurm queue manager
PHACT, PH ylogeny- A ware C omputation of T olerance (for amino acid substitutions), is a computational frame...
A snakemake for GTDB-tk
It uses GTDB-tk to taxonomically annotate your genomes and to build a tree. Run as follows:
dbdir="databases"
genome_dir="gen...
Pipeline for Constructing Species Phylogenies Using BUSCOs
Pipeline to construct species phylogenies using BUSCOs. The pipeline automatically creates the directory structure from the c...
NSGTree: A Fast and Simplified Phylogenetic Tree Construction Pipeline
v0.4.3 August 19 2023 New Simple Genome Tree (NSGTree) is a computational pipeline for fast and easy construction of phylo...
Houses a snakemake workflow used for multiple sequence alignment and maximum likelihood phylogeny construction of genes or proteins. Originally used to study sex determination genes in mosquitoes.
This snakemake file contains a workflow allowing the creation of MAFFT alignments and RAxML phylogenies. Inputs can either be...
Flexible workflow designed for bacterial WGS analyses (annotation, core/pan-genome reconstruction, phylogeny)
This pipeline is written specifically for annotating the bacteria whole genome sequences (WGS) . The pipeline handles mul...
Multi-species Coalescent Model for Phylogenetic Tree Inference with ASTRAL
In order to calculate phylogenetic trees, different methods can be used. One method concatenates multiple gene sequences ...
Ribosomal Protein Phylogenetic Tree Generator using Snakemake
# Ribosomal protein tree generation - Python Snakemake version A workflow to generate ribosomal protein phylogenetic trees, u...
Snakemake workflow for running maximum likelihood (ML) phylogenetic analysis using RAxML-NG and the associated tools. Provides much more accurate results than IQ-TREE based phylogenies.
Scalable RAxML-NG-based phylogenetic analysis using Snakemake This is a Snakemake workflow for running scalable maximum li...