iqtree2

Here are 5 public repositories matching this topic...

PathoGenOmics-Lab / snpick

snpick is a fast and memory-efficient Rust-based SNP extraction tool designed to handle large genomic alignments with minimal RAM usage and high-speed performance.

rust fast snps alignments fasta raxml phylogeny asc iqtree raxml-ng iqtree2 snp-sites snpick

Updated Sep 2, 2026
Rust

YuSugihara / ancseq

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Ancestral sequence reconstruction with gap-state inference using IQ-TREE

bioinformatics phylogenetics molecular-evolution multiple-sequence-alignment ancestral-sequence-reconstruction iqtree2

Updated Jul 26, 2026
Python

Qasim-Hussain-Code / ppanggolin_pangenomics_helicobacter_pylori

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Graph-based pangenomic and synteny analysis of Helicobacter pylori (n=41 complete RefSeq genomes) using PPanGGOLiN, with reproducible workflows for annotation (Prokka), ANI quality control (FastANI), core-genome phylogeny (MAFFT + IQ-TREE 2), resistome profiling (AMRFinderPlus), and publication-grade visualizations.

bioinformatics microbial-genomics comparative-genomics synteny phylogenomics pangenomics mafft resistome prokka fastani bacterial-genomics amrfinderplus iqtree2 helicobacter-pylori ppanggolin

Updated Aug 4, 2026
Python

TRAPS-Suite / TRAPS-Phylogeny

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nextflow phylogenetics iqtree2 epa-ng

Updated Jul 9, 2026
Nextflow

Anand-Research-Group / complex-I

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This repository contains a set of scripts and workflows designed to search for Respiratory Complex I (NADH Ubiquinone Oxidoreductase) subunits in prokaryotic genomes and proteomes.

bioinformatics biopython protein-sequences proteome homology-search mafft mmseqs2 fasttree prokaryotic-genomes hmmer3 species-distribution evalue-thresholds alphafold2 operons iqtree2 protein-sequences-tree

Updated Mar 23, 2026
Jupyter Notebook

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