Jambe

How to use the software

Version 1.0 alpha, December 2001

• Format of the DNA sequence alignment
• Format of the window control file
• Format of the MCMC control file
• Scratch file
• Start the program

Format of the DNA sequence alignment

Example:

4 100
strain1
ATGAACAACCAACGAAAAAAGACGGCTCGACCGTCTTTCAATATGCTGAA
ACGCGCGAGAAACCGCGTGTCAACTGGTTCACAGTTGGCGAAGAGATTCT
strain2
CAAAAGGATTGCTTTCAGGCCAAGGACCCATGAAATTGGTGATGGCTTTC
ATAGCATTCCTAAGATTTCTAGCCATACCCCCAACAGCAGGAATTTTGGC
strain3
TAGATGGGGCTCATTCAAGAAGAATGGAGCGATCAAAGTGCTACGGGGTT
TCAAGAAAGAAATCTCAAACATGTTGAACATAATGAATAGAAGGAAAAGA
strain4
TCTGTGACCATGCTCCTCATGCTGCTGCCCACAGCCTTGGCGTTCCATTT
GACTACACGAGGGGGAGAGCCACACATGATAGTTAGCAAGCAGGAAAGAG


Format of the window control file

Example:

1 500 10

Window length: 500. Window is moved in increments of 10 bases.

Format of the MCMC control file

Scratch file

Intermediate results are written out to the scratch file resultsAllTopos.out. This file must exist at the beginning of the simulation as an empty file. In UNIX, just give the command:

cat > resultsAllTopos.out
CTRL d

Start the program

Start the program with the command:

java Jambe

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Last modified: December 2001