run.pl has been extensively developed. Phylomarker now supports more than pairwise comparison.
Result files are now created by run.pl
Website and source code updated to v2.0.
Web tool now available (for small genomes only).
Spring 2009:
Source code has been tested quite extensively with a few bugs fixed.
2008:
Thaine Rowley took over the project.
Rewrote most of the source code to add in coverage and
identity. Also added in the statistics files.
Updated the webpage. Made a new layout for the updates
page, wrote new readme files, updated source code page.
Made a script to combine all the parts of the program.
You can now compare as many genomes as you want with one
command. Run.pl will be uploaded when V2.0 of the
program is released.
December 2006:
Updated website. Several sections were added,
including Source Code Download and Result Files.
Two new species of fish, Stickleback and Japanese
rice fish were compared. The results are available
in the Result Files section.
Fall 2006:
The manuscript was submitted for journal reviews.
Summer 2006:
Gong Zhang, another summer student of Guoqing, was
hired to continue Fred's work. Gong optimized the
scripts in two ways:
Gong's script can calculate coverage,
which is an effective parameter for
filtering exons of duplicated genes.
Gong's scripts produce a tablular output,
with GC-contents.
Spring 2006:
Writing the manuscript and performing data analysis.
Guoqing presented the result in the First
International Conference on Phylogenomics. March
16-19, 2006. Sainte-Adele, Quebec, Canada.
November 2005:
Guoqing received the UNO UCR First Award to work on
this project.
Fall 2005:
Sequencing more candidate markers on more fish.
Regular meetings on Saturday between Chenhong and
Guoqing discussing how to analyze data and how to
write the manuscript.
Summer 2005:
Fred Potmesil, a summer student of Guoqing, wrote
several scripts for filtering single-copy orthologs
between Zebrafish and Fugu. The script used bit
scores for filtering exons of duplicated genes.
Later it was found it was not an ideal parameter for
duplicated gene removal.
Chenhong tested a set of candidate markers and the
sequence data produced was encouraging.
Fall 2004:
Project began. Chenhong and Guoqing initiated this
project.