How to cite

You can cite the relevant papers (linked below, for each piece of data). Please & thank you.

Orthology inference with Possvm

Possvm is a python utility that identifies pairs and clusters of orthologous genes from gene phylogenies (Grau-Bové and Sebé-Pedrós, MBE 2021). It takes advantage of the species overlap algorithm implemented in the ETE toolkit to parse the phylogeny and identify orthologous gene pairs, and MCL clustering for orthogroup identification.

You can get the code and test data from these repositories:

Link	Description
	Source code and manual
	Test data from Grau-Bové and Sebé-Pedrós, MBE 2021.

Github repositories

Code and instructions for the following projects:

Link	Publication
	A phylogenetic and proteomic reconstruction of eukaryotic chromatin evolution (Grau-Bové et al., Nature Ecology and Evolution 2022, PDF available here upon reasonable HTTP request.
	Protein mixture models for common amino-acid recoding schemes (e.g. Dayhoff), for use in IQ-TREE.
	Resistance to pirimiphos-methyl in West African Anopheles is spreading via duplication and introgression of the Ace1 locus (Grau-Bové et al., Plos Genetics 2021).
	Evolution of the insecticide target Rdl in African Anopheles is driven by interspecific and interkaryotypic introgression (Grau-Bové et al., MBE 2020).
	Isolation and transcriptomic analysis of Anopheles gambiae oenocytes enables the delineation of hydrocarbon biosynthesis (Grigoraki et al., eLife 2020).
	Global transcriptome analysis of the aphelid Paraphelidium tribonemae supports the phagotrophic origin of fungi (Torruella et al., Communications Biology 2018).
	Origin of exon skipping-rich transcriptomes in animals driven by evolution of gene architecture (Grau-Bové et al., Genome Biology 2018). Genome annotation data and list of species.

Data

Data from Dynamics of genomic innovation in the unicellular ancestry of animals (Grau-Bové et al., eLife 2017).

Link	Description
	Supplementary data and figures. Includes phylogenomic alignments.
Figshare	Genome assembly and annotation of Corallochytrium limacisporum
Figshare	Genome assembly and annotation of Chromosphaera perkinsii
Figshare	Genome assembly and annotation of Ichthyophonus hoferi
Figshare	Genome assembly and annotation of Abeoforma whisleri
Figshare	Genome assembly and annotation of Pirum gemmata