1 # $Id: 00_phylogeny_factory.template,v 1.9 2008/11/25 22:25:52 cmzmasek Exp $
3 # Name convention if alignment specific parameters
4 # are to be used (such as HMMs for hmmalign):
5 # the substring before the first underscore is a
6 # unique identifier and needs to match the identifiers
7 # in '% <parameter-type> <unique-id>=<value>' statements
9 # alignment name : 'bcl2_new_alignment'
10 # parameter statments: '% HMM bcl2=Bcl2_ls'
12 $ PROBCONS=/home/czmasek/SOFTWARE/PROBCONS/probcons_v1_12/probcons
13 $ DIALIGN_TX=/home/czmasek/SOFTWARE/DIALIGNTX/DIALIGN-TX_1.0.1/source/dialign-tx
14 $ DIALIGN_DIR=/home/czmasek/SOFTWARE/DIALIGNTX/DIALIGN-TX_1.0.1/conf
15 $ MAFFT=/home/czmasek/SOFTWARE/MAFFT/mafft-6.240/src/mafft
16 $ T_COFFEE=/home/czmasek/SOFTWARE/T_COFFEE/T-COFFEE_distribution_Version_6.78/bin_linux/t_coffee
17 $ MUSCLE=/home/czmasek/SOFTWARE/MUSCLE/muscle3.7/muscle
18 $ CLUSTALW=/home/czmasek/SOFTWARE/CLUSTALW/clustalw-2.0.9/src/clustalw2
19 $ KALIGN=/home/czmasek/SOFTWARE/KALIGN/kalign203/kalign
20 $ HMMALIGN=/home/czmasek/SOFTWARE/HMMER/hmmer-2.3.2/src/hmmalign
21 $ MSA_PRO=/home/czmasek/SOFTWARE/FORESTER/DEV/forester-atv/ruby/evoruby/exe/msa_pro.rb
22 $ PHYLO_PL=/home/czmasek/SOFTWARE/FORESTER/DEV/forester-atv/perl/phylo_pl.pl
24 # Default value is 40.
31 % PHYLO_OPT=-WIB100q@1nxbwS21
33 % TMP_DIR = /home/czmasek/tmp/
35 # Need to give full path for HMM files.
36 % HMM NACHT=/home/czmasek/DATA/PFAM/NACHT_ls_cz.hmm
37 % HMM TIR=/home/czmasek/DATA/PFAM/PFAM_LS/TIR.ls.hmm
38 % HMM SRCR=/home/czmasek/DATA/PFAM/PFAM_LS/SRCR.ls.hmm
39 % HMM Homeobox=/home/czmasek/DATA/PFAM/PFAM_LS/Homeobox.ls.hmm
40 % HMM Cofilin_ADF=/home/czmasek/DATA/PFAM/PFAM_LS/Cofilin_ADF.ls.hmm
43 > KALIGN $ -o $_kalign
44 > MSA_PRO -o=p -n=10 -rr=0.5 -rsl=%[RSL]% $_kalign $_kalign_05_%[RSL]%.aln
45 > MSA_PRO -o=n -n=10 -rr=0.5 -rsl=%[RSL]% $_kalign $_kalign_05_%[RSL]%.nex
46 > PHYLO_PL %[PHYLO_OPT]% $_kalign_05_%[RSL]%.aln $_kalign_05_%[RSL]% %[TMP_DIR]%
49 > HMMALIGN -q -m -o $_hmmalign_m %[HMM]% $
50 > MSA_PRO -o=p -n=10 -rr=0.5 -c -rsl=%[RSL]% $_hmmalign_m $_hmmalign_m_05_%[RSL]%.aln
51 > MSA_PRO -o=n -n=10 -rr=0.5 -c -rsl=%[RSL]% $_hmmalign_m $_hmmalign_m_05_%[RSL]%.nex
52 > PHYLO_PL %[PHYLO_OPT]% $_hmmalign_m_05_%[RSL]%.aln $_hmmalign_m_05_%[RSL]% %[TMP_DIR]%
55 > HMMALIGN -q -o $_hmmalign %[HMM]% $
56 > MSA_PRO -o=p -n=10 -rr=0.5 -c -rsl=%[RSL]% $_hmmalign $_hmmalign_05_%[RSL]%.aln
57 > MSA_PRO -o=n -n=10 -rr=0.5 -c -rsl=%[RSL]% $_hmmalign $_hmmalign_05_%[RSL]%.nex
58 > PHYLO_PL %[PHYLO_OPT]% $_hmmalign_05_%[RSL]%.aln $_hmmalign_05_%[RSL]% %[TMP_DIR]%
61 > PROBCONS $ > $_probcons
62 > MSA_PRO -o=p -n=10 -rr=0.5 -c -rsl=%[RSL]% $_probcons $_probcons_05_%[RSL]%.aln
63 > MSA_PRO -o=n -n=10 -rr=0.5 -c -rsl=%[RSL]% $_probcons $_probcons_05_%[RSL]%.nex
64 > PHYLO_PL %[PHYLO_OPT]% $_probcons_05_%[RSL]%.aln $_probcons_05_%[RSL]% %[TMP_DIR]%
67 > DIALIGN_TX DIALIGN_DIR $ $_dialigntx
68 > MSA_PRO -o=p -n=10 -rr=0.5 -c -rsl=%[RSL]% $_dialigntx $_dialigntx_05_%[RSL]%.aln
69 > MSA_PRO -o=n -n=10 -rr=0.5 -c -rsl=%[RSL]% $_dialigntx $_dialigntx_05_%[RSL]%.nex
70 > PHYLO_PL %[PHYLO_OPT]% $_dialigntx_05_%[RSL]%.aln $_dialigntx_05_%[RSL]% %[TMP_DIR]%
73 > MAFFT --maxiterate 1000 --localpair --quiet $ > $_mafft
74 > MSA_PRO -o=p -n=10 -rr=0.5 -c -rsl=%[RSL]% $_mafft $_mafft_05_%[RSL]%.aln
75 > MSA_PRO -o=n -n=10 -rr=0.5 -c -rsl=%[RSL]% $_mafft $_mafft_05_%[RSL]%.nex
76 > PHYLO_PL %[PHYLO_OPT]% $_mafft_05_%[RSL]%.aln $_mafft_05_%[RSL]% %[TMP_DIR]%
79 #> T_COFFEE $ -outfile $_tcoffee
81 #> MSA_PRO -o=p -n=10 -rr=0.5 -c -rsl=%[RSL]% $_tcoffee $_tcoffee_05_%[RSL]%.aln
82 #> MSA_PRO -o=n -n=10 -rr=0.5 -c -rsl=%[RSL]% $_tcoffee $_tcoffee_05_%[RSL]%.nex
83 #> PHYLO_PL %[PHYLO_OPT]% $_tcoffee_05_%[RSL]%.aln $_tcoffee_05_%[RSL]% %[TMP_DIR]%
88 > MUSCLE -maxiters 1000 -maxtrees 100 -clw -in $ -out $_muscle
89 > MSA_PRO -o=p -n=10 -rr=0.5 -c -rsl=%[RSL]% $_muscle $_muscle_05_%[RSL]%.aln
90 > MSA_PRO -o=n -n=10 -rr=0.5 -c -rsl=%[RSL]% $_muscle $_muscle_05_%[RSL]%.nex
91 > PHYLO_PL %[PHYLO_OPT]% $_muscle_05_%[RSL]%.aln $_muscle_05_%[RSL]% %[TMP_DIR]%
94 > CLUSTALW $ -outfile=$_clustalw
96 > MSA_PRO -o=p -n=10 -rr=0.5 -c -rsl=%[RSL]% $_clustalw $_clustalw_05_%[RSL]%.aln
97 > MSA_PRO -o=n -n=10 -rr=0.5 -c -rsl=%[RSL]% $_clustalw $_clustalw_05_%[RSL]%.nex
98 > PHYLO_PL %[PHYLO_OPT]% $_clustalw_05_%[RSL]%.aln $_clustalw_05_%[RSL]% %[TMP_DIR]%