Add GLprobs and MSAprobs to binaries

[jabaws.git] / binaries / src / MSAProbs-0.9.7 / README

diff --git a/binaries/src/MSAProbs-0.9.7/README b/binaries/src/MSAProbs-0.9.7/README
new file mode 100644 (file)
index 0000000..5114c85
--- /dev/null
+++ b/binaries/src/MSAProbs-0.9.7/README
@@ -0,0 +1,48 @@
+\r
+MSAPROBS is a new and practial protein multiple sequence alignment\r
+algorithm based on pair hidden markov model and partition function\r
+posterrior probabilities. Assessed on BAliBASE 3.0, PREFAB 4.0,\r
+SABMARK 1.65, and OXBENCH, MSAProbs achieves the statistically \r
+highest alignment accuracy, compared to ClustalW 2.0.10, MAFFT 6.717(\r
+using L-INS-i with --maxiterate = 1000), MUSCLE 3.8.31, ProbCons 1.12,\r
+and Probalign 1.3. (current version 0.9.3, March 17, 2010).\r
+\r
+\r
+To use this software, please cite the following paper:\r
+/******************************************************\r
+Yongchao Liu, Bertil Schmidt, Douglas L. Maskell:\r
+\r
+"MSAProbs: multiple sequence alignment based on \r
+pair hidden Markov models and partition function posterior probabilities",\r
+\r
+Bioinformatics 2010, 26(16): 1958-1964\r
+\r
+*******************************************************/\r
+\r
+This software is developed by Liu Yongchao, School of Computer Engineering,\r
+Nanyang Technological University. If any comments or problems, \r
+please directly contact Liu Yongchao using either of the following email \r
+addresses: liuy0039@ntu.edu.sg; nkcslyc@hotmail.com.\r
+\r
+MSAPROBS is an open-source software, complying with General Public \r
+Licence (GPL) version 3.0. MSAPROBS is distributed WITHOUT WARRANTY, express or\r
+implied. The authors accept NO LEGAL LIABILITY OR  RESPONSIBILITY  for\r
+loss due to reliance on the program.\r
+\r
+(1) Linux and Windows are supported, with a Makefile and a Visual Studio 2005\r
+project co-existing in the source code tarball.\r
+\r
+Change to sub-directory MSAProbs, the Makefile file for Linux can be found.\r
+\r
+(2)The default compiling options enable OpenMP support to fully utlized the \r
+compute capability of multi-core CPUs, as multi-core CPUs have been commonplace.\r
+\r
+Typical Usage:\r
+ (1) "./msaprobs -help" or "./msaprobs -?"\r
+                       Get the command line options\r
+\r
+ (2) "./msaprobs infile >outfile" or "./msaprobs infile -o outfile"\r
+                       The alignments are printed out into file "outfile" in FASTA format\r
+\r
+ (3) ./msaprobs infile -o outfile -num_threads 4\r
+                       Use four threads to accelerate the execution\r