# $Id: 00_phylogeny_factory.template,v 1.9 2008/11/25 22:25:52 cmzmasek Exp $

# Name convention if alignment specific parameters
# are to be used (such as HMMs for hmmalign):
#  the substring before the first underscore is a
#  unique identifier and needs to match the identifiers
#  in '% <parameter-type> <unique-id>=<value>' statements 
#  Example:
#  alignment name     : 'bcl2_new_alignment'
#  parameter statments: '% HMM bcl2=Bcl2_ls' 
#                       '% RSL bcl2=60' 
$ PROBCONS=/home/czmasek/SOFTWARE/PROBCONS/probcons_v1_12/probcons
$ DIALIGN_TX=/home/czmasek/SOFTWARE/DIALIGNTX/DIALIGN-TX_1.0.1/source/dialign-tx
$ DIALIGN_DIR=/home/czmasek/SOFTWARE/DIALIGNTX/DIALIGN-TX_1.0.1/conf
$ MAFFT=/home/czmasek/SOFTWARE/MAFFT/mafft-6.240/src/mafft
$ T_COFFEE=/home/czmasek/SOFTWARE/T_COFFEE/T-COFFEE_distribution_Version_6.78/bin_linux/t_coffee
$ MUSCLE=/home/czmasek/SOFTWARE/MUSCLE/muscle3.7/muscle
$ CLUSTALW=/home/czmasek/SOFTWARE/CLUSTALW/clustalw-2.0.9/src/clustalw2
$ KALIGN=/home/czmasek/SOFTWARE/KALIGN/kalign203/kalign
$ HMMALIGN=/home/czmasek/SOFTWARE/HMMER/hmmer-2.3.2/src/hmmalign
$ MSA_PRO=/home/czmasek/SOFTWARE/FORESTER/DEV/forester-atv/ruby/evoruby/exe/msa_pro.rb
$ PHYLO_PL=/home/czmasek/SOFTWARE/FORESTER/DEV/forester-atv/perl/phylo_pl.pl 

# Default value is 40.
% RSL SRCR=50
% RSL NACHT=50
% RSL TIR=60
% RSL Bcl2=100
% RSL homeobox=40

% PHYLO_OPT=-WIB100q@1nxbwS21

% TMP_DIR  = /home/czmasek/tmp/

# Need to give full path for HMM files.
% HMM NACHT=/home/czmasek/DATA/PFAM/NACHT_ls_cz.hmm
% HMM TIR=/home/czmasek/DATA/PFAM/PFAM_LS/TIR.ls.hmm
% HMM SRCR=/home/czmasek/DATA/PFAM/PFAM_LS/SRCR.ls.hmm
% HMM Homeobox=/home/czmasek/DATA/PFAM/PFAM_LS/Homeobox.ls.hmm
% HMM Cofilin_ADF=/home/czmasek/DATA/PFAM/PFAM_LS/Cofilin_ADF.ls.hmm


> KALIGN $ -o $_kalign
> MSA_PRO -o=p -n=10 -rr=0.5 -rsl=%[RSL]% $_kalign $_kalign_05_%[RSL]%.aln
> MSA_PRO -o=n -n=10 -rr=0.5 -rsl=%[RSL]% $_kalign $_kalign_05_%[RSL]%.nex
> PHYLO_PL %[PHYLO_OPT]% $_kalign_05_%[RSL]%.aln $_kalign_05_%[RSL]% %[TMP_DIR]%
- 

> HMMALIGN -q -m -o $_hmmalign_m %[HMM]% $ 
> MSA_PRO -o=p -n=10 -rr=0.5 -c -rsl=%[RSL]% $_hmmalign_m $_hmmalign_m_05_%[RSL]%.aln
> MSA_PRO -o=n -n=10 -rr=0.5 -c -rsl=%[RSL]% $_hmmalign_m $_hmmalign_m_05_%[RSL]%.nex
> PHYLO_PL %[PHYLO_OPT]% $_hmmalign_m_05_%[RSL]%.aln $_hmmalign_m_05_%[RSL]% %[TMP_DIR]%
- 

> HMMALIGN -q -o $_hmmalign %[HMM]% $ 
> MSA_PRO -o=p -n=10 -rr=0.5 -c -rsl=%[RSL]% $_hmmalign $_hmmalign_05_%[RSL]%.aln
> MSA_PRO -o=n -n=10 -rr=0.5 -c -rsl=%[RSL]% $_hmmalign $_hmmalign_05_%[RSL]%.nex
> PHYLO_PL %[PHYLO_OPT]% $_hmmalign_05_%[RSL]%.aln $_hmmalign_05_%[RSL]% %[TMP_DIR]%
- 

> PROBCONS $ > $_probcons
> MSA_PRO -o=p -n=10 -rr=0.5 -c -rsl=%[RSL]% $_probcons $_probcons_05_%[RSL]%.aln
> MSA_PRO -o=n -n=10 -rr=0.5 -c -rsl=%[RSL]% $_probcons $_probcons_05_%[RSL]%.nex
> PHYLO_PL %[PHYLO_OPT]% $_probcons_05_%[RSL]%.aln $_probcons_05_%[RSL]% %[TMP_DIR]%
-  
    
> DIALIGN_TX DIALIGN_DIR $ $_dialigntx
> MSA_PRO -o=p -n=10 -rr=0.5 -c -rsl=%[RSL]% $_dialigntx $_dialigntx_05_%[RSL]%.aln
> MSA_PRO -o=n -n=10 -rr=0.5 -c -rsl=%[RSL]% $_dialigntx $_dialigntx_05_%[RSL]%.nex
> PHYLO_PL %[PHYLO_OPT]% $_dialigntx_05_%[RSL]%.aln $_dialigntx_05_%[RSL]% %[TMP_DIR]%
-
    
> MAFFT --maxiterate 1000 --localpair --quiet $ > $_mafft
> MSA_PRO -o=p -n=10 -rr=0.5 -c -rsl=%[RSL]% $_mafft $_mafft_05_%[RSL]%.aln
> MSA_PRO -o=n -n=10 -rr=0.5 -c -rsl=%[RSL]% $_mafft $_mafft_05_%[RSL]%.nex
> PHYLO_PL %[PHYLO_OPT]% $_mafft_05_%[RSL]%.aln $_mafft_05_%[RSL]% %[TMP_DIR]%
-
    
#> T_COFFEE $ -outfile $_tcoffee
#> rm $.dnd
#> MSA_PRO -o=p -n=10 -rr=0.5 -c -rsl=%[RSL]% $_tcoffee $_tcoffee_05_%[RSL]%.aln
#> MSA_PRO -o=n -n=10 -rr=0.5 -c -rsl=%[RSL]% $_tcoffee $_tcoffee_05_%[RSL]%.nex
#> PHYLO_PL %[PHYLO_OPT]% $_tcoffee_05_%[RSL]%.aln $_tcoffee_05_%[RSL]% %[TMP_DIR]%
#> rm $.dnd
#> rm $.html
#-
    
> MUSCLE  -maxiters 1000 -maxtrees 100 -clw -in $ -out $_muscle
> MSA_PRO -o=p -n=10 -rr=0.5 -c -rsl=%[RSL]% $_muscle $_muscle_05_%[RSL]%.aln
> MSA_PRO -o=n -n=10 -rr=0.5 -c -rsl=%[RSL]% $_muscle $_muscle_05_%[RSL]%.nex
> PHYLO_PL %[PHYLO_OPT]%  $_muscle_05_%[RSL]%.aln  $_muscle_05_%[RSL]% %[TMP_DIR]%
-

> CLUSTALW $ -outfile=$_clustalw
> rm $.dnd
> MSA_PRO -o=p -n=10 -rr=0.5 -c -rsl=%[RSL]% $_clustalw $_clustalw_05_%[RSL]%.aln
> MSA_PRO -o=n -n=10 -rr=0.5 -c -rsl=%[RSL]% $_clustalw $_clustalw_05_%[RSL]%.nex
> PHYLO_PL %[PHYLO_OPT]% $_clustalw_05_%[RSL]%.aln $_clustalw_05_%[RSL]% %[TMP_DIR]%
> rm $.dnd
-