pull cactus
pull reference libs
First stab at adding phyloP support
pull hal
pull clapack
update readme and pull hal
pull hal
add three Kent binaries that hal2assemblyHub.py depends on
pull latest development submodules
pull cactus2hal
add hgGcPercent from kent tools
pull phast
pull ucsc modules. always turn on phyloP support by default since it no longer conflicts twith udc
pull cactus
pull hal
Provide an option to give a hostname for connections to the ktserver
Merge branch 'master' into allowFixedInternalNodes
Misc work from the last month, only interesting thing is root outgroup stuff