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README 2011-12-01 2.9 kB 22 weekly downloads
probmask.tar.gz 2011-12-01 112.4 kB 55 weekly downloads
zorro_linux_x86_64 2011-12-01 126.4 kB 11 weekly downloads
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ZORRO : A probabilistic alignment masking program Authors: Martin Wu, Sourav Chatterji and Jonathan Eisen 1. Prerequisites Compiling ZORRO needs the C compiler gcc (preferably version 4.1.2 or later) Running ZORRO needs perl 2. Installation You can either download the precompiled executables from http://sourceforge.net/projects/probmask/files/ zorro_linux_x86_64 for Linux zorro_mac for Mac or you can download the source code probmask.tar.gz and compile it yourself To compile, on the command line, type tar -zxvf probmask.tar.gz cd probmask/trunk/ ./autogen.sh ./configure --prefix=$HOME make install The binary "zorro" will be produced and installed to $HOME/bin directory. Optional : To easily access ZORRO from the command line, add the directory containing ZORRO ($HOME/bin) to your environment variable $PATH. Note: If you download the executables, make sure first change the file permission by typing "chmod +x zorro_mac' or 'chmod +x zorro_linux_x86_64'. You also need to have FastTree installed and in your system's executable path. 3. Running ZORRO ZORRO is run as: "zorro [options] inputfile > outputfile" Input : Here the input file is multiple sequence alignment in multi fasta format. More details about this format can be found at http://en.wikipedia.org/wiki/FASTA_format An example input file is provided in: Example/family_15833_5_prank2_2_cDNAid Output : The output is a plain text file with confidence scores of one column per line, in order from column 1, 2, 3 ... etc. The confidence score is a measure of the reliability of a column according to a pair-HMM model. It has a value between 0 and 10. An example output fle is provided in: Example/family_15833_5_prank2_2_cDNAid.mask Options: ZORRO has several options which are listed below and can also be accessed by typing "zorro -h". -sample : Sampling pairs to calculate alignment reliabilty [Off By Default] -nosample : No Sampling i.e. using every pair to calculate alignment reliabilty [On By Default] -noweighting : Using sum of pairs instead of weighted sum of pairs to calculate column confidence [Off By Default] -ignoregaps : Ignore pair-gaps in columns when calculating column confidences [Off By Default] -Nsample NUMBER : Tells ZORRO to sample #NUMBER pairs when sampling, automatically turns on -sample option [Samples 10*Nseq sequences By Default] -treeprog PROGRAM: Tells ZORRO to use PROGRAM instead of the default FastTree to create guide tree [FastTree By Default] -guide treefile : User provided guide tree 4. Usage example zorro -sample ./Example/family_15833_5_prank2_2_cDNAid > family_15833_5_prank2_2_cDNAid.mask 5. Contact Martin Wu (mw4yv@virginia.edu) Sourav Chatterji (souravc@gmail.com) Jonathan Eisen (jaeisen@ucdavis.edu) 6. Other credits ZORRO makes use of FastTree, a GPL program available from: http://www.microbesonline.org/fasttree/
Source: README, updated 2011-12-01