peaselab / mvftools

mvftools

Authors

• James B. Pease (website: http://www.peaselab.org (@jamesbpease)
• Ben K. Rosenzweig

Contributors

• Roddra Johnson
• Ellen Weinheimer

Description

Multisample Variant Format (MVF), which is designed for compact storage and efficient analysis of multi-genome and multi-transcriptome datasets. The programs provided in MVFtools support this format, both with conversion utilities, filtering and transformation programs, and data analysis and visualization modules. MVF format is designed specifically for biological data analysis, since sequence data is encoded based on the information content at a particular aligned sequence site. This contextual encoding allows for rapid computation of phylogenetic and population genetic analyses, and small file sizes that enable data sharing and distribution.

Citation Information

Pease JB and BK Rosenzweig. 2018. "Encoding Data Using Biological Principles: the Multisample Variant Format for Phylogenomics and Population Genomics" IEEE/ACM Transactions on Computational Biology and Bioinformatics. 15(4):1231-1238. http://www.dx.doi.org/10.1109/tcbb.2015.2509997

Please also include the URL https://www.github.com/jbpease/mvftools in your methods section where the program is referenced.

(Note this paper was originally published online in 2015, but did not receive final citation page numbering until 2018. You may see older citations as 2015, which is the same paper.)

Manual

Please see the full HTML manual: https://github.com/peaselab/mvftools/blob/main/doc/mvftools.html

Or the PDF Manual: https://github.com/peaselab/mvftools/blob/main/doc/mvftools.pdf

Requirements

MVFtools requires:

• Python 3.x but can be run on any operating system. (Python 2.x will NOT work)
• BioPython: https://biopython.org/
• Numpy: https://www.numpy.org/
• Scipy: https://www.scipy.org/
• MatplotLib: https://www.matplotlib.org/

Optionally required for certain modules:

• RAxML-ng: https://github.com/amkozlov/raxml-ng
• RAxML: 8.2+; https://sco.h-its.org/exelixis/web/software/ raxml/index.html
• PAML: http://abacus.gene.ucl.ac.uk/software/paml.html

FAQ and Questions/Comments

See the manual for Frequently Asked Questions and other discussion commentary. For questions, contact James Pease by email (info at http://www.peaselab.org)

Examples of papers that have used MVFtools

• http://dx.doi.org/10.1111/mec.13679
• http://dx.doi.org/10.1111/mec.13610
• http://dx.doi.org/10.1371/journal.pbio.1002379
• https://doi.org/10.1038/s41467-018-04963-6
• https://doi.org/10.1093/gbe/evy227
• https://doi.org/10.1093/molbev/msy198
• https://doi.org/10.1534/genetics.118.301831
• https://doi.org/10.1111/mec.14877
• https://doi.org/10.1186/s13059-018-1471-8
• https://doi.org/10.1093/molbev/msaa148

License

This file is part of MVFtools.

MVFtools is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

MVFtools is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with Foobar. If not, see (http://www.gnu.org/licenses/).