Supplementary information of the paper:

Combining Multiple Datasets in a Likelihood Analysis: Which Models are Best?

by Tal Pupko, Dorothee Huchon, Ying Cao, Norihiro Okada and Masami Hasegawa

Accession numbers of the sequences

Sequence alignments (fasta format):

Madsen data set: A2AB, BRCA1, IRBP, vWF

Murphy data set: ADORA3, ATP7A, BDNF, CNR1, EDG1, ZFX

Mitochondrial data set: ND1, ND2, COX1, COX2, ATP8, ATP6, COX3, ND3, ND4L, ND4, ND5, Cytb

Tree topologies

Likelihood results (Microsoft Excel files):

Madsen data set

Murphy data set

Mitochondrial data set

AIC results:

Madsen data set

Murphy data set

Mitochondrial data set

Program:

Download the program combine.zip, PC executable, version 1.01, last updated 31 March 2003.

Usage:

For the computation of tree likelihood the program name must be followed by the command file name (i.e. combine command.txt)

For the computation of Kishino-Hasegawa test the program name must be followed by two command files

(i.e. combine command1.txt command2.txt)

Command file (explanations, example)