About

Phylociraptor is a bioinformatics pipeline to create phylogenomic trees for a specified set of species using different alignment, trimming and tree reconstruction methods. Installation is simple with only two dependencies. It is very scalable and runs on Linux/Unix machines, servers as well as HPC clusters.

Phylociraptor performs every step of a typical phylogenomic analysis.

  • It automatically downloads genomes available on NCBI and combines them with additional specified genomes provided by the user.

  • It identifies single-copy orthologs for a set of genomes (locally provided or downloaded automatically).

  • It creates alignments for single-copy genes.

  • It allows to trim and filter alignments in various ways.

  • It calculates gene-trees for each alignment.

  • It creates a species tree from gene-trees using ASTRAL.

  • It creates Neighbor-Joining trees using quicktree.

  • It calculates the best substitution model for single-gene alignments.

  • It automatically produces all input and runs iqtree and raxml to create concatenated Maximum-Likelihood phylogenies.

  • It provides extensive reports for each analysis step combined in a single HTML file which can be viewed in a Web Browser.

  • Most steps are highly parallelized and it is possible to get from a list of hundreds of taxa to a phylogenomic tree in a few days.

Phylociraptor has the following dependencies:

General:

dependencies:

Only Singularity and Snakemake need to be installed. All other software comes in containerized form and no installation is necessary.

Orthology inference:

Alignment:

Trimming:

Tree inference: