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Open Access Highly Accessed Research article

The phylogeny of the mammalian heme peroxidases and the evolution of their diverse functions

Noeleen B Loughran1, Brendan O'Connor2, Ciarán Ó'Fágáin2 and Mary J O'Connell12*

Author Affiliations

1 Bioinformatics and Molecular Evolution Group, School of Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland

2 School of Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland

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BMC Evolutionary Biology 2008, 8:101  doi:10.1186/1471-2148-8-101

Published: 27 March 2008

Additional files

Additional file 1:

The resultant site stripped multiple sequence alignment of MHP sequences. This figure depicts the multiple sequence alignment that was selected following RMSD analysis. This alignment has sites of rate category 8, 7, and 6 removed.

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Open Data

Additional file 2:

RMSD nodal distance between each site-stripped MHP phylogeny and the ideal phylogeny. This table summarizes the results of the statistical comparison (RMSD) of the ideal phylogeny with each site stripped phylogeny. Values closer to zero are closer to complete agreement, the alignment with site categories 8 through to 6 removed, is the phylogeny closest to ideal.

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Open Data

Additional file 3:

Parameter estimates and likelihood scores of one ratio and site-specific models. The data presented in this table are the results of ML analysis of site specific evolutionary models applied to the MHP alignment. The name of the model is given in column 1, the number of parameters estimated is given in column 2, the Log likelihood value in column 3, and the parameter estimates in column 4 and 5.

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Additional file 4:

Parameter estimates and likelihood scores for branch-site models: MPO and EPO clades. This table summarizes the results of ML analysis on the MHP data, using branch specific models of evolution. The MPO and EPO clades are treated as foreground lineages independently and all other peroxidase clades as background. The LRTs are performed between model A and M1 and model B and M3K2 from Additional file 3.

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Open Data

Additional file 5:

Parameter estimates and likelihood scores for branch-site models: LPO and TPO clades. This table summarizes the results of ML analysis on the MHP data, using branch specific models of evolution. The LPO and TPO clades are treated as foreground lineages independently and all other peroxidase clades as background. The LRTs are performed between model A and M1 and model B and M3K2 from Additional file 3.

Format: DOC Size: 35KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data