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phyloSkeleton: taxon selection, data retrieval and marker identification for phylogenomics
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. (Guy)ORCID iD: 0000-0001-8354-2398
2017 (English)In: Bioinformatics, ISSN 1367-4803, E-ISSN 1367-4811, Vol. 33, no 8, p. 1230-1232Article in journal (Refereed) Published
Abstract [en]

With the wealth of available genome sequences, a difficult and tedious part of inferring phylogenomic trees is now to select genomes with an appropriate taxon density in the different parts of the tree. The package described here offers tools to easily select the most representative organisms, following a set of simple rules based on taxonomy and assembly quality, to retrieve the genomes from public databases (NCBI, JGI), to annotate them if necessary, to identify given markers in these, and to prepare files for multiple sequence alignment.

AVAILABILITY AND IMPLEMENTATION: phyloSkeleton is a Perl module and is freely available under GPLv3 at https://bitbucket.org/lionelguy/phyloskeleton/ CONTACT: lionel.guy@imbim.uu.se.

Place, publisher, year, edition, pages
2017. Vol. 33, no 8, p. 1230-1232
National Category
Bioinformatics and Systems Biology
Identifiers
URN: urn:nbn:se:uu:diva-312601DOI: 10.1093/bioinformatics/btw824ISI: 000400985900020PubMedID: 28057682OAI: oai:DiVA.org:uu-312601DiVA, id: diva2:1064232
Available from: 2017-01-12 Created: 2017-01-12 Last updated: 2017-06-19Bibliographically approved

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