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Phylogenetic orthology inference for comparative genomics
Make colorful identity heatmaps of genomic sequence
A telomere-to-telomere toolkit for gap-free genome assembly and centromeric repeat identification
General tools for genomic analyses.
(Not Offical) BBMap short read aligner, and other bioinformatic tools.
Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
CGView is a Java package for generating high-quality, zoomable maps of circular genomes.
MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. For documentation and downloading the program, please see the home page:
Automatically exported from code.google.com/p/jmodeltest2
A tool for automated alignment trimming in large-scale phylogenetic analyses. Development version: 2.0
Organelle Genome Assembly Toolkit (Chloroplast/Mitocondrial/ITS)
Randomly subsample sequencing reads or alignments
Inference of ploidy and heterozygosity structure using whole genome sequencing data
tbenavi1 / genomescope2.0
Forked from schatzlab/genomescopeReference-free profiling of polyploid genomes
LTR_retriever is a highly accurate and sensitive program for identification of LTR retrotransposons; The LTR Assembly Index (LAI) is also included in this package.
RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.
dnaPipeTE (for de-novo assembly & annotation Pipeline for Transposable Elements), is a pipeline designed to find, annotate and quantify Transposable Elements in small samples of NGS datasets. It is…
Converts a VCF file to a FASTA alignment provided a reference genome and a GFF file
Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis
Tools for fast and flexible genome assembly scaffolding and improvement