mashtree

Mashtree is a command line tool designed to analyze the similarity between multiple genomes or metagenomes. It uses the Mash algorithm, which is based on MinHash sketches, to efficiently compute pairwise distances and generate clustering trees.

The tool takes input in fasta, fastq, or raw read formats and internally pre-processes the sequences by filtering out low-complexity regions and homopolymers. It then generates MinHash sketches for each sequence, representing the overall content of the genome/metagenome in a compact form.

Mashtree then compares these sketches using the Jaccard index, which measures the similarity between two sets, to compute pairwise distances. It uses these distances to build a hierarchical clustering tree, wherein closely related genomes/metagenomes are grouped together.

The resulting tree can be visualized using Newick format and can provide insights into the genetic relatedness and diversity among the input sequences. This can be useful in various biological applications, such as taxonomic classification, comparative genomics, and metagenomic analysis.

Mashtree is a powerful and efficient tool for performing large-scale genomic or metagenomic comparisons, enabling researchers to gain valuable insights into the relationships between different genomes or metagenomes.