From: cmzmasek@gmail.com Date: Sat, 22 Dec 2012 04:57:06 +0000 (+0000) Subject: not needed anymore X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=d01c8980bbdf27f7c21119ae86b3209a9dcee1b4;p=jalview.git not needed anymore --- diff --git a/forester/archive/RIO/COPYRIGHT b/forester/archive/RIO/COPYRIGHT deleted file mode 100644 index eae6883..0000000 --- a/forester/archive/RIO/COPYRIGHT +++ /dev/null @@ -1,32 +0,0 @@ -RIO - Phylogenomic Protein Function Analysis -Copyright (C) 2002 Washington University School of Medicine -and Howard Hughes Medical Institute -All rights reserved ----------------------------------------------------------------- - -This pipeline of programs is free software. You can redistribute it -and/or modify it under the terms of the GNU General Public License as -published by the Free Software Foundation; either version 2 of the -License, or (at your option) any later version. - -In other words, you are free to modify, copy, or redistribute this -source code and its documentation in any way you like, but you must -distribute all derivative versions as free software under the same -terms that I've provided my code to you (i.e. the GNU General Public -License). This precludes any use of the code in proprietary or -commercial software unless your source code is made freely available. - -In contrast to RIO as a whole, the JAVA programs in directory "java" -are under the BSD license. - -This software is distributed in the hope that it will be useful, but -WITHOUT ANY WARRANTY; without even the implied warranty of -MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU -General Public License for more details. - -You should have received a copy of the GNU General Public License -along with this RIO release, in the file LICENSE; if not, write to -the Free Software Foundation, Inc., 675 Mass. Ave, Cambridge, MA 02139 -USA. - - diff --git a/forester/archive/RIO/IMPORTANT_NOTICE b/forester/archive/RIO/IMPORTANT_NOTICE deleted file mode 100644 index 9040c6f..0000000 --- a/forester/archive/RIO/IMPORTANT_NOTICE +++ /dev/null @@ -1,48 +0,0 @@ -RIO - Phylogenomic Protein Function Analysis ----------------------------------------------------------------- - - -RIO contains modified versions of programs written by others: - -1. TREE-PUZZLE - (Strimmer, K., and A. von Haeseler. 1996. Quartet puzzling: A quartet maximum - likelihood method for reconstructing tree topologies. Mol. Biol. Evol. 13: 964-969.) - - -2. PHYLIP - (Felsenstein, J. 1993. PHYLIP (Phylogeny Inference Package) version 3.5c. - Distributed by the author. - Department of Genetics, University of Washington, Seattle.) - - -Please note: ------------- - -1. RIO uses modifications of these programs, the original versions were - written by others: - - TREE-PUZZLE: Heiko A. Schmidt, Korbinian Strimmer, Martin Vingron, Arndt von Haeseler - - PHYLIP: Joseph Felsenstein, see also http://evolution.genetics.washington.edu/phylip/credits.html - - -2. The programs in the RIO distribution have been modified specifically - to work within RIO and cannot be used for any other purpose. - - -3. I am responsible for any accidentally introduced errors. - - -4. The original can be downloaded from the following sites: - TREE-PUZZLE: http://www.tree-puzzle.de/ - PHYLIP: http://evolution.genetics.washington.edu/phylip.html - - -RIO also contains hmmer (version 2.2g). -hmmer can be downloaded at: http://hmmer.wustl.edu/ - - - -Christian Zmasek, 03/09/02 - - diff --git a/forester/archive/RIO/LICENSE b/forester/archive/RIO/LICENSE deleted file mode 100644 index a43ea21..0000000 --- a/forester/archive/RIO/LICENSE +++ /dev/null @@ -1,339 +0,0 @@ - GNU GENERAL PUBLIC LICENSE - Version 2, June 1991 - - Copyright (C) 1989, 1991 Free Software Foundation, Inc. - 675 Mass Ave, Cambridge, MA 02139, USA - Everyone is permitted to copy and distribute verbatim copies - of this license document, but changing it is not allowed. - - Preamble - - The licenses for most software are designed to take away your -freedom to share and change it. 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If this is what you want to do, use the GNU Library General -Public License instead of this License. diff --git a/forester/archive/RIO/RIO_INSTALL b/forester/archive/RIO/RIO_INSTALL deleted file mode 100644 index 7d4f2ec..0000000 --- a/forester/archive/RIO/RIO_INSTALL +++ /dev/null @@ -1,459 +0,0 @@ - -RIO - Phylogenomic Protein Function Analysis - -____________________________________________ - - - - -RIO/FORESTER : http://www.genetics.wustl.edu/eddy/forester/ -RIO webserver: http://www.rio.wustl.edu/ - -Reference: Zmasek C.M. and Eddy S.R. (2002) - RIO: Analyzing proteomes by automated phylogenomics using - resampled inference of orthologs. - BMC Bioinformatics 3:14 - http://www.biomedcentral.com/1471-2105/3/14/ - - It is highly recommended that you read this paper before - installing and/or using RIO. (Included in the RIO - distribution as PDF: "RIO.pdf".) - - -Preconditions: A Unix system, Java 1.2 or higher, Perl, gcc or cc, - ... and some experience with Perl and Unix. - - - -1. Compilation -______________ - - -This describes how to compile the various components of RIO. - - - "gunzip RIO1.x.tar.gz" - - "tar -xvf RIO1.x.tar" - - - - -in directory "RIO1.x/C": - - "make" - - - -in directory "RIO1.x/hmmer" (version of HMMER is "2.2g"): - -(if you already have a local copy of HMMER 2.2g installed, this step -is not necessary, but in this case you need to change variables "$HMMALIGN", -"$HMMSEARCH", "$HMMBUILD", "$HMMFETCH", and "$SFE" to point to the -corresponding HMMER programs) - - "./configure" - - "make" - - - -in directory "RIO1.x/java" (requires JDK 1.2 or greater): - - "javac forester/tools/*java" - - "javac ATVapp.java" - - - - -in directory "RIO1.x/puzzle_dqo": - - "./configure" - - "make" - - - -in directory "RIO1.x/puzzle_mod": - - "./configure" - - "make" - - - -in directory "RIO1.x/phylip_mod/src": - - "make install" - - - - -2. Setting the variables in "RIO1.x/perl/rio_module.pm" -_______________________________________________________ - - -Most global variables used in "RIO1.x/perl/rio.pl" are set in -the perl module "RIO1.x/perl/rio_module.pm". -This module pretty much "controls everything". - -It is necessary to set the variables which point to: - --- the rio directory itself: $PATH_TO_FORESTER - - (example: $PATH_TO_FORESTER = "/home/czmasek/linux/RIO1.1/";) - - --- your Java virtual machine: $JAVA - - (example: $JAVA = "/home/czmasek/linux/j2sdk1.4.0/bin/java";) - - --- a directory where temporary files can be created: $TEMP_DIR_DEFAULT - - - - Example: - Now that $PATH_TO_FORESTER, $JAVA, $TEMP_DIR_DEFAULT are set, - it is posssible to run rio.pl based on the example precalculated distances - in "/example_data/": - - % RIO1.1/perl/rio.pl 1 A=aconitase Q=RIO1.1/LEU2_HAEIN N=QUERY_HAEIN O=out0 p I - - To use RIO to analyze your protein sequences, please continue setting - variables and preparing data...... - - - --- your local copy of the Pfam database (see http://pfam.wustl.edu/) - (if only precalculated distances are being used, these variables do not - matter): - - $PFAM_FULL_DIRECTORY -- the directory containing the "full" alignments - (Pfam-A.full) see below (3.) - - $PFAM_SEED_DIRECTORY -- the directory containing the "seed" alignments - (Pfam-A.seed) see below (3.) - - $PFAM_HMM_DB -- the Pfam HMM library file (Pfam_ls) - see below (3.) - - --- $TREMBL_ACDEOS_FILE and $SWISSPROT_ACDEOS_FILE: see below (4. and 5.). - - --- list of species (SWISS-PROT codes) which can be analyzed: $SPECIES_NAMES_FILE - (for most purposes $PATH_TO_FORESTER."data/species/tree_of_life_bin_1-4_species_list" - should be sufficient, hence this variable does not necessarly need to be changed) - - --- a default species tree in NHX format: $SPECIES_TREE_FILE_DEFAULT - (for most purposes $PATH_TO_FORESTER."data/species/tree_of_life_bin_1-4.nhx" - should be sufficient, hence this variable does not necessarly need to be changed) - - --- Only if precalculated distances are being used: - $MATRIX_FOR_PWD, $RIO_PWD_DIRECTORY, $RIO_BSP_DIRECTORY, - $RIO_NBD_DIRECTORY, $RIO_ALN_DIRECTORY, and $RIO_HMM_DIRECTORY: - please see below (6.) - - - - - - -IMPORTANT: Need to redo steps 3., 4., 5., and 6. if species - in the master species tree and/or the species list - are added and/or changed or if a new version of Pfam is used!! - - - - - -3. Downloading and processing of Pfam -_____________________________________ - - - -Please note: Even if you already have a local copy of the -Pfam database, you still need to perform steps c. through k. - -a. download - - "Pfam_ls" (PFAM HMM library, glocal alignment models) - - "Pfam-A.full" (full alignments of the curated families) - - "Pfam-A.seed" (seed alignments of the curated families) - [and ideally "prior.tar.gz"] - from http://pfam.wustl.edu/ or ftp.genetics.wustl.edu/pub/eddy/pfam-x/ - -b. "gunzip" and "tar -xvf" these downloaded files, if necessary - -c. create a new directory named "Full" and move "Pfam-A.full" into it - -d. in directory "Full" execute "RIO1.x/perl/pfam2slx.pl Pfam-A.full" - -e. set variable $PFAM_FULL_DIRECTORY in "RIO1.x/perl/rio_module.pm" - to point to this "Full" directory - -f. create a new directory named "Seed" and move "Pfam-A.seed" into it - -g. in directory "Seed" execute "RIO1.x/perl/pfam2slx.pl Pfam-A.seed" - -h. set variable $PFAM_SEED_DIRECTORY in "RIO1.x/perl/rio_module.pm" - to point to this "Seed" directory - -i. execute "RIO1.x/hmmer/binaries/hmmindex Pfam_ls" (in same - directory as "Pfam_ls") resulting in "Pfam_ls.ssi" - -j. set environment variable HMMERDB to point to the directory where - "Pfam_ls" and "Pfam_ls.ssi" reside - (for example "setenv HMMERDB /home/czmasek/PFAM7.3/") - -k. set variable $PFAM_HMM_DB in "RIO1.x/perl/rio_module.pm" - to point to the "Pfam_ls" file - (for example $PFAM_HMM_DB = "/home/czmasek/PFAM7.3/Pfam_ls";) - - - - -4. Extraction of ID, DE, and species from a SWISS-PROT sprot.dat file -_____________________________________________________________________ - - -This creates the file from which RIO will get the sequence descriptions for -sequences from SWISS-PROT. -(RIO1.x/data/ does not contain an example for this, since SWISS-PROT is -copyrighted.) - - -a. download SWISS-PROT "sprotXX.dat" from - "ftp://ca.expasy.org/databases/swiss-prot/release/" - -b. "extractSWISS-PROT.pl [species list]" - - ("extractSWISS-PROT.pl" is in "RIO1.x/perl") - - example: - "extractSWISS-PROT.pl sprot40.dat sp40_ACDEOS RIO1.x/data/species/tree_of_life_bin_1-4_species_list" - -c. the output file should be placed in "RIO1.x/data" and the - variable $SWISSPROT_ACDEOS_FILE in "RIO1.x/perl/rio_module.pm" should point - to this output. - - - - -5. Extraction of AC, DE, and species from a TrEMBL trembl.dat file -__________________________________________________________________ - - -This creates the file from which RIO will get the sequence descriptions for -sequences from TrEMBL. -(RIO1.x/data/ already contains an example: "trembl20_ACDEOS_1-4") - -a. download TrEMBL "trembl.dat.gz" from - "ftp://ca.expasy.org/databases/sp_tr_nrdb/" - -b. "gunzip trembl.dat.gz" - -c. "extractTrembl.pl [species list]" - - ("extractTrembl.pl" is in "RIO1.x/perl") - - example: - "extractTrembl.pl trembl.dat trembl17.7_ACDEOS_1-4 RIO1.x/data/species/tree_of_life_bin_1-4_species_list" - -d. the output file should be placed in "RIO1.x/data/" and the - variable $TREMBL_ACDEOS_FILE in "RIO1.x/perl/rio_module.pm" should point - to this output. - - - -Now, you could go to directly to 7. to run the examples...... - - - -6. Precalculation of pairwise distances (optional): pfam2pwd.pl -_______________________________________________________________ - - -This step is of course only necessary if you want to use RIO on -precalculated pairwise distances. The precalculation is time consuming -(range of one or two weeks on ten processors). -It is best to run it on a few machines, dividing up the input data. - -The program to do this, is "RIO1.x/perl/pfam2pwd.pl". - -Please note: "pfam2pwd.pl" creates a logfile in the same directory - where is places the pairwise distance output ($MY_RIO_PWD_DIRECTORY). - - - -The following variables in "RIO1.x/perl/pfam2pwd.pl" need to be set -("pfam2pwd.pl" gets most of its information from "rio_module.pm"): - - -"$MY_PFAM_FULL_DIRECTORY": - This is the directory where the Pfam full alignments reside, processed - as described in 3.a to 3.d. - - - -"$ALGNS_TO_USE_LIST_FILE": - If left empty, all alignments in $MY_PFAM_FULL_DIRECTORY are being - used the calculate pairwise distances from. - If this points to a file listing names of Pfam alignments, - only those listed are being used. - The file can either be a simple new-line deliminated list, or can have - the same format as the "Summary of changes" list - ("FI PF03214 RGP NEW SEED HMM_ls HMM_fs FULL DESC") - which is part of the Pfam distribution. - One purpose of this is to use the list of "too large" alignments - in the logfile produced by "pfam2pwd.pl" to run "pfam2pwd.pl" with - a smaller species list (as can be set with "$MY_SPECIES_NAMES_FILE") - on large alignments. - - - -"$MY_SPECIES_NAMES_FILE" -- Dealing with too large alignments: - - This is most important. It determines the species whose sequences - are being used (sequences from species not listed in $MY_SPECIES_NAMES_FILE - are ignored). Normally, one would use the same list as RIO uses - ($SPECIES_NAMES_FILE in "rio_module.pm"): - - my $MY_SPECIES_NAMES_FILE = $SPECIES_NAMES_FILE; - - For certain large families (such as protein kinases, one must use - a species file which contains less species in order to be able to finish - the calculations in reasonable time: - - my $MY_SPECIES_NAMES_FILE = $PATH_TO_FORESTER."data/tree_of_life_bin_1-4_species_list_NO_RAT_RABBIT_MONKEYS_APES_SHEEP_GOAT_HAMSTER - - An additional way to reduce the number of sequences in an alignment is - to only use sequences originating from SWISS-PROT. This is done by - placing the following line of code into pfam2pwd.pl: - - $TREMBL_ACDEOS_FILE = $PATH_TO_FORESTER."data/NO_TREMBL"; - - - -"$MY_RIO_PWD_DIRECTORY", -"$MY_RIO_BSP_DIRECTORY", -"$MY_RIO_NBD_DIRECTORY", -"$MY_RIO_ALN_DIRECTORY", -"$MY_RIO_HMM_DIRECTORY": - These determine where to place the output. - After all the data has been calculated, the corresponding variables - in RIO1.x/perl/rio_module.pm ("$RIO_PWD_DIRECTORY", etc.) need to be set - so that they point to the appropriate values. Having different variables - allows to precalculate distances and at the same time use RIO on - previously precalculated distances. - - - -"$MY_TEMP_DIR": - A directory to create temporary files in. - - - -"$MIN_SEQS": - Alignments in which the number of sequences after pruning (determined - by "$MY_SPECIES_NAMES_FILE") is lower than $MIN_SEQS, are ignored - (no calculation of pwds). - - - -"$MAX_SEQS": - Alignments in which the number of sequences after pruning (determined - by "$MY_SPECIES_NAMES_FILE") is greater than $MAX_SEQS, are ignored - (no calculation of pwds). - - - -"$MY_SEED": - Seed for the random number generator for bootstrapping (must be 4n+1). - - - -"$MY_MATRIX": - This is used to choose the model to be used for the (ML) - distance calculation: - 0 = JTT - 2 = BLOSUM 62 - 3 = mtREV24 - 5 = VT - 6 = WAG - PAM otherwise - After all the data has been calculated, variable "$MATRIX_FOR_PWD" - in RIO1.x/perl/rio_module.pm needs to be set to the same value. - - - -Once pairwise distances are calculated, the following variables in -"rio_module.pm" need to be set accordingly: -$MATRIX_FOR_PWD : corresponds to $MY_MATRIX in pfam2pwd.pl -$RIO_PWD_DIRECTORY : corresponds to $MY_RIO_PWD_DIRECTORY in pfam2pwd.pl -$RIO_BSP_DIRECTORY : corresponds to $MY_RIO_BSP_DIRECTORY in pfam2pwd.pl -$RIO_NBD_DIRECTORY : corresponds to $MY_RIO_NBD_DIRECTORY in pfam2pwd.pl -$RIO_ALN_DIRECTORY : corresponds to $MY_RIO_ALN_DIRECTORY in pfam2pwd.pl -$RIO_HMM_DIRECTORY : corresponds to $MY_RIO_HMM_DIRECTORY in pfam2pwd.pl -...of course, if Pfam has been updated, the corresponding variables in rio_module.pm -($PFAM_FULL_DIRECTORY, etc.) need to be updated, too. - - - - - - -IMPORTANT: Need to redo steps 3., 4., 5., and 6. if species - in the master species tree and/or the species list - are added and/or changed or if a new version of Pfam is used! - - - - -7. Example of a phylogenomic analysis using "rio.pl" -____________________________________________________ - - -Without using precalculated distances (for this, all the variables above -need to point to the correct loctions, in particular to your local and processed -Pfam database): - - % RIO1.1/perl/rio.pl 3 A=/path/to/my/pfam/Full/aconitase H=aconitase Q=RIO1.1/LEU2_HAEIN N=QUERY_HAEIN O=out3 p I C E - - - -Without using precalculated distances (for this, all the variables above -need to point to the correct loctions, in particular to your local and processed -Pfam database) using a query sequence which is already in the alignment: - - % RIO1.1/perl/rio.pl 4 A=/path/to/my/pfam/Full/aconitase N=LEU2_LACLA/5-449 O=out4 p I C E - - - -Using the example precalculated distances in "/example_data/" -($RIO_PWD_DIRECTORY, etc. need to point to $PATH_TO_FORESTER."example_data/"): - - % RIO1.1/perl/rio.pl 1 A=aconitase Q=RIO1.1/LEU2_HAEIN N=QUERY_HAEIN O=out1 p I C E - - - -Using a query sequence which is already in the precalculated distances in "/example_data/" -($RIO_PWD_DIRECTORY, etc. need to point to $PATH_TO_FORESTER."example_data/"): - - % RIO1.1/perl/rio.pl 2 A=aconitase N=LEU2_LACLA/5-449 O=out2 p I C E - - - -for detailed instructions on how to use rio.pl see the source code, -or type "rio.pl" without any arguments - - - - -Christian Zmasek -zmasek@genetics.wustl.edu -05/26/02 - diff --git a/forester/archive/RIO/data.tar.bz2 b/forester/archive/RIO/data.tar.bz2 deleted file mode 100644 index d5a86af..0000000 Binary files a/forester/archive/RIO/data.tar.bz2 and /dev/null differ diff --git a/forester/archive/RIO/docs/RIO.pdf b/forester/archive/RIO/docs/RIO.pdf deleted file mode 100644 index 546b02d..0000000 Binary files a/forester/archive/RIO/docs/RIO.pdf and /dev/null differ