Comparative genomics Tools

Infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences.

GFAffix identifies walk-preserving shared affixes in variation graphs and collapses them into a non-redundant graph structure.

GenMap is a fast and exact tool for computing genome mappability, calculating the uniqueness of k-mers across genomic positions while allowing for a specified number of mismatches, helping identify unique and repetitive genomic regions.

HMMER is used for searching sequence databases for sequence homologs, and for making sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs).

A fast and effective stochastic algorithm to infer phylogenetic trees by maximum likelihood. IQ-TREE compares favorably to RAxML and PhyML in terms of likelihoods with similar computing time

ISMapper searches for IS positions in sequence data using paired end Illumina short reads, an IS query/queries of interest and a reference genome. ISMapper reports the IS positions it has found in each isolate, relative to the provided reference genome.

Adopts model selection and model averaging to calculate nonsynonymous (Ka) and synonymous (Ks) substitution rates, attempting to include as many features as needed for accurately capturing evolutionary information in protein-coding sequences. In addition, several existing methods for calculating Ka and Ks are also incorporated into KaKs_Calculator.

LAST is a sequence alignment tool that finds and aligns related regions between large biological sequences, supporting DNA-DNA, DNA-protein, and protein-protein comparisons with sensitivity comparable to BLAST but with greater speed and flexibility for large datasets.

Lambda is a local aligner optimized for many query sequences and searches in protein space. It is compatible to BLAST, but much faster than BLAST and many other comparable tools.

An accurate gene annotation mapping tool.

LiftoffTools is a toolkit for comparing gene annotations mapped between genome assemblies, enabling the detection and analysis of gene sequence variants, synteny, and gene copy number changes. It leverages Liftoff for annotation transfer and offers modules for analyzing protein-coding genes, gene synteny, and gene copy number.

MCScanX is a toolkit that implements an adjusted MCScan algorithm for detecting gene synteny and collinearity across multiple genomes, incorporating 14 utility programs for visualization and downstream evolutionary analyses including chromosome structural changes and gene family expansion history.

MUMmer4 is an ultrafast genome alignment system for aligning large-scale genomic sequences. It uses suffix trees and maximal unique matches (MUMs) to rapidly find alignments between complete genomes, enabling comparison of closely or distantly related genomes.

Fast genome and metagenome distance estimation using MinHash.

MashTree is a fast command-line tool for creating phylogenetic trees from genome assemblies or raw reads using Mash distances, enabling rapid whole-genome phylogeny estimation without traditional sequence alignment.

Mauve is a program for performing comaparative analyses of genomes. To generate a new genome alignment with Mauve, select 'Align' from the File menu. To open an existing genome alignment, select 'Open' from the file menu.

MetaCHIP is a horizontal gene transfer (HGT) identification pipeline that combines best-match and phylogenetic approaches to detect community-level HGT events in microbial genomes.

Miniprot aligns a protein sequence against a genome with affine gap penalty, splicing and frameshift. It is primarily intended for annotating protein-coding genes in a new species using known genes from other species.

Circos is tool for visualizing data in a circular format. It was developed for genomic data but can work for many other kinds of data as well.

The Environment for Tree Exploration (ETE) is a computational framework that simplifies the reconstruction, analysis, and visualization of phylogenetic trees and multiple sequence alignments. Here, we present ETE v3, featuring numerous improvements in the underlying library of methods, and providing a novel set of standalone tools to perform common tasks in comparative genomics and phylogenetics. The new features include (i) building gene-based and supermatrix-based phylogenies using a single command, (ii) testing and visualizing evolutionary models, (iii) calculating distances between trees of different size or including duplications, and (iv) providing seamless integration with the NCBI taxonomy database. ETE is freely available at http://etetoolkit.org

gfatools is a set of tools for manipulating sequence graphs in the GFA or the rGFA format. It has implemented parsing, subgraph and conversion to FASTA/BED.