Homo version 1.3

Collection Title:

Homo version 1.3

Collection Description:

A program for analysing compositional heterogeneity across aligned sequence data. Most model-based molecular phylogenetic methods assume evolution under stationary, reversible, and globally homogeneous conditions, implying that it would be unwise to use these methods if the data evolved under more complex conditions. Homo allows users to test whet... moreher pairs of sequences in alignments of nucleotides or amino acids are consistent with evolution under stationary, reversible, and globally homogeneous conditions (for details, see Ababneh et al. 2006b). The output is a: Brief summary (printed to the terminal); Full summary (printed to a file); Five tables (printed to files), one with the p-values and four with the compositional distances. The summaries allow users to determine whether some of the sequences violate the assumption of evolution under stationary, reversible, and globally homogeneous conditions. For further details, see the manual, which is included with the software. less

Field of Research:

Bioinformatics ;  Bioinformatics Software

DOI:

https://doi.org/10.4225/08/5a56c7a9e4c2a

Contact:CSIRO Enquiries
 CSIROEnquiries@csiro.au
 1300 363 400
Keywords:

Homo 1.3 Software ;  Bioinformatics ;  nucleotide sequences ;  phylogenetic tree

Related Links:

:	Homo code repository on GitHub
:	Rouse GW, Jermiin LS, Wilson NG, Eeckhaut I, Lanterbecq D, Oji T, Young CM, Browning T, Cisternas P, Helgen LE, Stuckey M, Messing CG. 2013. Fixed, free and fixed: The fickle phylogeny of extant Crinoidea (Echinodermata) and their Permian-Triassic origin. Mol. Phylogen. Evol. 66, 161-181.

Supporting Files:

Homo-1.3_Licence.pdf

Credit:

This software was developed by Lars S Jermiin while employed at CSIRO and the University of Sydney. Currently, LSJ is at Research School of Biology, The Australian National University, Acton, ACT 2601, Australia (lars.jermiin@anu.edu.au). Homo uses four functions (i.e., xGaussian_Distribution_Tail, xChi_Square_Distribution_Tail, Sum_Poisson_Terms, and Sum_Over_Odd_Terms) from two source code files (i.e., gaussian_distribution_tail.c, and chi-square_distribution_tail.c) written by Dr Richard L. Horn (athretprogr@gmail.com). Dr Horn granted CSIRO and USYD a license to use these source code files without restrictions. The functions provided by Dr Horn replace some of the functions made available to the public from his Mathematics Source Library C & ASM (http://www.mymathlib.com).

Licence:

CSIRO Open Source Software Licence (Based on MIT/BSD Open Source Licence)

Organisations:

CSIRO (Australia), University of Sydney (Australia)

Attribution Statement:

Jermiin, Lars (2017): Homo version 1.3. v1. CSIRO. Software Collection. https://doi.org/10.4225/08/5a56c7a9e4c2a

Rights Statement:

All Rights (including copyright) CSIRO, University of Sydney 2017.

Access:

The metadata and files (if any) are available to the public.