When you use the programs here, please cite the following paper:
Yoshihito Niimura, Masatoshi Nei (2007) Extensive gains and losses of olfactory receptor genes in mammalian evolution. PLoS ONE 2: e708.
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The method to obtain the result in Figure 1D of Niimura and Nei (2007) is explained here.
You first need to download LINTREE from
Prof. Naoko Takezaki's website.
Then, please compile the C program named 'branchout.c'.
branchout cladeP.njboot -o 1 2 3 4 5 6 7 8 > cladeP.branchoutYou obtain the output file 'cladeP.branchout'.
'1 2 3 4 5 6 7 8' means the outgroup gene numbers.
Now you can use the program 'mrcacount.pl' for estimating the numbers of ancestral genes and gene
mrcacount.pl cladeP.branchout spetree.dat cladeP.genelist -b 350 > cladeP.mrca'spetree.dat' indicates the phylogeny of the species examined.
In this example, the content of this file is:
Human~Macaq~Mouse~Rat~Dog~Cow~Oposs Platy 0Each line corresponds to one node of a species tree.
This file contains seven lines, because there are seven nodes at which the number of ancestral genes was estimated (see Fig. 2A).
For example, the second line represents a node for the separation between opossum and placentals (including Human, Macaq, Mouse, Rat, Dog, Cow). Platypus is the outgroup for this node.
'0' indicates the outgroup of all mammals. Therefore, the first line corresponds to a node for the separation between the platypus and opossum+placentals.
'cladeP.genelist' shows correspondence between gene names and species names.
'cladeP.mrca' is the result in Figure 1D.
Last updated: August 26, 2019