# HG changeset patch # User rnateam # Date 1433842563 14400 # Node ID 7e55ac3bd4585882f3f853986f80407d167e39ed Uploaded diff -r 000000000000 -r 7e55ac3bd458 compalignp.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/compalignp.xml Tue Jun 09 05:36:03 2015 -0400 @@ -0,0 +1,48 @@ + + Fractional identities between alignments + + compalignp + + + + + + + $output +]]> + + + + + + + + + + + + + + + + + Paranoia version of squids compalign. + +Compute fractional "identity" between trusted alignment and test alignment +Identity of the multiple sequence alignments is defined as +the averaged identity over all N(N-1)/2 pairwise alignments. + + +]]> + + + 10.1186/1748-7188-1-19 + + diff -r 000000000000 -r 7e55ac3bd458 test-data/eukaryotic-trnas_2.1.clustal --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/eukaryotic-trnas_2.1.clustal Tue Jun 09 05:36:03 2015 -0400 @@ -0,0 +1,7 @@ +CLUSTAL 2.1 multiple sequence alignment + + +Anolis_carolinensis_chrUn_GL34 TGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTAGTGGGATCGATGCCCACATTCTCCA +Anolis_carolinensis_chrUn_GL35 GGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGCGAGAGGTAGCGGGATTGATGCCCGCATTCTCCA + ************************************** ************** ******* ********* + diff -r 000000000000 -r 7e55ac3bd458 test-data/eukaryotic-trnas_2.1.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/eukaryotic-trnas_2.1.out Tue Jun 09 05:36:03 2015 -0400 @@ -0,0 +1,1 @@ +1.00 diff -r 000000000000 -r 7e55ac3bd458 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Tue Jun 09 05:36:03 2015 -0400 @@ -0,0 +1,27 @@ + + + + + + + + + http://www.biophys.uni-duesseldorf.de/bralibase/compalignp.tgz + + + + + + make + + compalignp + $INSTALL_DIR/bin + + + $INSTALL_DIR/bin + $INSTALL_DIR/bin + + + + +