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Bader-Research · Dec 18, 2020 · 6e431ab · 6e431ab
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diff --git a/Binaries/Alpha-Binaries/Clustalw/clustalw b/Binaries/Alpha-Binaries/Clustalw/clustalw
diff --git a/Binaries/Alpha-Binaries/Fasta/fasta34 b/Binaries/Alpha-Binaries/Fasta/fasta34
diff --git a/Binaries/Alpha-Binaries/Glimmer/glimmer2 b/Binaries/Alpha-Binaries/Glimmer/glimmer2
diff --git a/Binaries/Alpha-Binaries/Hmmer/hmmsearch b/Binaries/Alpha-Binaries/Hmmer/hmmsearch
diff --git a/Binaries/Alpha-Binaries/Phylip/dnapenny b/Binaries/Alpha-Binaries/Phylip/dnapenny
diff --git a/Binaries/Alpha-Binaries/Phylip/promlk b/Binaries/Alpha-Binaries/Phylip/promlk
diff --git a/Binaries/Alpha-Binaries/Predator/predator b/Binaries/Alpha-Binaries/Predator/predator
diff --git a/Binaries/PowerPc-Binaries/Blast/BLOSUM62 b/Binaries/PowerPc-Binaries/Blast/BLOSUM62
@@ -0,0 +1,31 @@
+#  Matrix made by matblas from blosum62.iij
+#  * column uses minimum score
+#  BLOSUM Clustered Scoring Matrix in 1/2 Bit Units
+#  Blocks Database = /data/blocks_5.0/blocks.dat
+#  Cluster Percentage: >= 62
+#  Entropy =   0.6979, Expected =  -0.5209
+   A  R  N  D  C  Q  E  G  H  I  L  K  M  F  P  S  T  W  Y  V  B  Z  X  *
+A  4 -1 -2 -2  0 -1 -1  0 -2 -1 -1 -1 -1 -2 -1  1  0 -3 -2  0 -2 -1  0 -4 
+R -1  5  0 -2 -3  1  0 -2  0 -3 -2  2 -1 -3 -2 -1 -1 -3 -2 -3 -1  0 -1 -4 
+N -2  0  6  1 -3  0  0  0  1 -3 -3  0 -2 -3 -2  1  0 -4 -2 -3  3  0 -1 -4 
+D -2 -2  1  6 -3  0  2 -1 -1 -3 -4 -1 -3 -3 -1  0 -1 -4 -3 -3  4  1 -1 -4 
+C  0 -3 -3 -3  9 -3 -4 -3 -3 -1 -1 -3 -1 -2 -3 -1 -1 -2 -2 -1 -3 -3 -2 -4 
+Q -1  1  0  0 -3  5  2 -2  0 -3 -2  1  0 -3 -1  0 -1 -2 -1 -2  0  3 -1 -4 
+E -1  0  0  2 -4  2  5 -2  0 -3 -3  1 -2 -3 -1  0 -1 -3 -2 -2  1  4 -1 -4 
+G  0 -2  0 -1 -3 -2 -2  6 -2 -4 -4 -2 -3 -3 -2  0 -2 -2 -3 -3 -1 -2 -1 -4 
+H -2  0  1 -1 -3  0  0 -2  8 -3 -3 -1 -2 -1 -2 -1 -2 -2  2 -3  0  0 -1 -4 
+I -1 -3 -3 -3 -1 -3 -3 -4 -3  4  2 -3  1  0 -3 -2 -1 -3 -1  3 -3 -3 -1 -4 
+L -1 -2 -3 -4 -1 -2 -3 -4 -3  2  4 -2  2  0 -3 -2 -1 -2 -1  1 -4 -3 -1 -4 
+K -1  2  0 -1 -3  1  1 -2 -1 -3 -2  5 -1 -3 -1  0 -1 -3 -2 -2  0  1 -1 -4 
+M -1 -1 -2 -3 -1  0 -2 -3 -2  1  2 -1  5  0 -2 -1 -1 -1 -1  1 -3 -1 -1 -4 
+F -2 -3 -3 -3 -2 -3 -3 -3 -1  0  0 -3  0  6 -4 -2 -2  1  3 -1 -3 -3 -1 -4 
+P -1 -2 -2 -1 -3 -1 -1 -2 -2 -3 -3 -1 -2 -4  7 -1 -1 -4 -3 -2 -2 -1 -2 -4 
+S  1 -1  1  0 -1  0  0  0 -1 -2 -2  0 -1 -2 -1  4  1 -3 -2 -2  0  0  0 -4 
+T  0 -1  0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -2 -1  1  5 -2 -2  0 -1 -1  0 -4 
+W -3 -3 -4 -4 -2 -2 -3 -2 -2 -3 -2 -3 -1  1 -4 -3 -2 11  2 -3 -4 -3 -2 -4 
+Y -2 -2 -2 -3 -2 -1 -2 -3  2 -1 -1 -2 -1  3 -3 -2 -2  2  7 -1 -3 -2 -1 -4 
+V  0 -3 -3 -3 -1 -2 -2 -3 -3  3  1 -2  1 -1 -2 -2  0 -3 -1  4 -3 -2 -1 -4 
+B -2 -1  3  4 -3  0  1 -1  0 -3 -4  0 -3 -3 -2  0 -1 -4 -3 -3  4  1 -1 -4 
+Z -1  0  0  1 -3  3  4 -2  0 -3 -3  1 -1 -3 -1  0 -1 -3 -2 -2  1  4 -1 -4 
+X  0 -1 -1 -1 -2 -1 -1 -1 -1 -1 -1 -1 -1 -1 -2  0  0 -2 -1 -1 -1 -1 -1 -4 
+* -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4  1 
diff --git a/Binaries/PowerPc-Binaries/Blast/blastall b/Binaries/PowerPc-Binaries/Blast/blastall
diff --git a/Binaries/PowerPc-Binaries/Ce/CE b/Binaries/PowerPc-Binaries/Ce/CE
diff --git a/Binaries/PowerPc-Binaries/Ce/pom/mkDB b/Binaries/PowerPc-Binaries/Ce/pom/mkDB
diff --git a/Binaries/PowerPc-Binaries/Ce/pom/mkDB_sgi b/Binaries/PowerPc-Binaries/Ce/pom/mkDB_sgi
diff --git a/Binaries/PowerPc-Binaries/Ce/pom/mkDB_sun b/Binaries/PowerPc-Binaries/Ce/pom/mkDB_sun
diff --git a/Binaries/PowerPc-Binaries/Clustalw/clustalw b/Binaries/PowerPc-Binaries/Clustalw/clustalw
diff --git a/Binaries/PowerPc-Binaries/Clustalw/clustalw-smp b/Binaries/PowerPc-Binaries/Clustalw/clustalw-smp
diff --git a/Binaries/PowerPc-Binaries/Fasta/fasta34_t b/Binaries/PowerPc-Binaries/Fasta/fasta34_t
diff --git a/Binaries/PowerPc-Binaries/Fasta/ssearch34_t b/Binaries/PowerPc-Binaries/Fasta/ssearch34_t
diff --git a/Binaries/PowerPc-Binaries/Glimmer/build-icm b/Binaries/PowerPc-Binaries/Glimmer/build-icm
diff --git a/Binaries/PowerPc-Binaries/Glimmer/extract b/Binaries/PowerPc-Binaries/Glimmer/extract
diff --git a/Binaries/PowerPc-Binaries/Glimmer/get-putative b/Binaries/PowerPc-Binaries/Glimmer/get-putative
diff --git a/Binaries/PowerPc-Binaries/Glimmer/glimmer.icm b/Binaries/PowerPc-Binaries/Glimmer/glimmer.icm
diff --git a/Binaries/PowerPc-Binaries/Glimmer/glimmer2 b/Binaries/PowerPc-Binaries/Glimmer/glimmer2
diff --git a/Binaries/PowerPc-Binaries/Glimmer/long-orfs b/Binaries/PowerPc-Binaries/Glimmer/long-orfs
diff --git a/Binaries/PowerPc-Binaries/Glimmer/run-glimmer2 b/Binaries/PowerPc-Binaries/Glimmer/run-glimmer2
@@ -0,0 +1,16 @@
+echo "run Glimmer2"
+clear
+echo "Genome is " $1
+echo "Find non-overlapping orfs in  tmp.coord"
+rm -f tmp.coord
+long-orfs $1 | get-putative >tmp.coord
+echo "Extract training sequences to  tmp.train"
+rm -f tmp.train
+extract $1 tmp.coord >tmp.train
+wc tmp.train
+echo "Build interpolated context model in  tmp.model"
+rm -f tmp.model
+build-icm <tmp.train >tmp.model
+echo "Predict genes with Glimmer2 with coordinates in  g2.coord"
+rm -f g2.coord
+glimmer2 $1 tmp.model | get-putative >g2.coord
diff --git a/Binaries/PowerPc-Binaries/Grappa/grappa b/Binaries/PowerPc-Binaries/Grappa/grappa
diff --git a/Binaries/PowerPc-Binaries/Hmmer/hmmpfam b/Binaries/PowerPc-Binaries/Hmmer/hmmpfam
diff --git a/Binaries/PowerPc-Binaries/Hmmer/hmmsearch b/Binaries/PowerPc-Binaries/Hmmer/hmmsearch
diff --git a/Binaries/PowerPc-Binaries/Phylip/dnapenny b/Binaries/PowerPc-Binaries/Phylip/dnapenny
diff --git a/Binaries/PowerPc-Binaries/Phylip/infile b/Binaries/PowerPc-Binaries/Phylip/infile
diff --git a/Binaries/PowerPc-Binaries/Phylip/promlk b/Binaries/PowerPc-Binaries/Phylip/promlk
diff --git a/Binaries/PowerPc-Binaries/Predator/predator b/Binaries/PowerPc-Binaries/Predator/predator
diff --git a/Binaries/PowerPc-Binaries/Predator/stride.dat b/Binaries/PowerPc-Binaries/Predator/stride.dat
diff --git a/Binaries/PowerPc-Binaries/Tcoffee/lalign2list b/Binaries/PowerPc-Binaries/Tcoffee/lalign2list
diff --git a/Binaries/PowerPc-Binaries/Tcoffee/t_coffee b/Binaries/PowerPc-Binaries/Tcoffee/t_coffee
diff --git a/Binaries/x86-Binaries/Blast/BLOSUM62 b/Binaries/x86-Binaries/Blast/BLOSUM62
@@ -0,0 +1,31 @@
+#  Matrix made by matblas from blosum62.iij
+#  * column uses minimum score
+#  BLOSUM Clustered Scoring Matrix in 1/2 Bit Units
+#  Blocks Database = /data/blocks_5.0/blocks.dat
+#  Cluster Percentage: >= 62
+#  Entropy =   0.6979, Expected =  -0.5209
+   A  R  N  D  C  Q  E  G  H  I  L  K  M  F  P  S  T  W  Y  V  B  Z  X  *
+A  4 -1 -2 -2  0 -1 -1  0 -2 -1 -1 -1 -1 -2 -1  1  0 -3 -2  0 -2 -1  0 -4 
+R -1  5  0 -2 -3  1  0 -2  0 -3 -2  2 -1 -3 -2 -1 -1 -3 -2 -3 -1  0 -1 -4 
+N -2  0  6  1 -3  0  0  0  1 -3 -3  0 -2 -3 -2  1  0 -4 -2 -3  3  0 -1 -4 
+D -2 -2  1  6 -3  0  2 -1 -1 -3 -4 -1 -3 -3 -1  0 -1 -4 -3 -3  4  1 -1 -4 
+C  0 -3 -3 -3  9 -3 -4 -3 -3 -1 -1 -3 -1 -2 -3 -1 -1 -2 -2 -1 -3 -3 -2 -4 
+Q -1  1  0  0 -3  5  2 -2  0 -3 -2  1  0 -3 -1  0 -1 -2 -1 -2  0  3 -1 -4 
+E -1  0  0  2 -4  2  5 -2  0 -3 -3  1 -2 -3 -1  0 -1 -3 -2 -2  1  4 -1 -4 
+G  0 -2  0 -1 -3 -2 -2  6 -2 -4 -4 -2 -3 -3 -2  0 -2 -2 -3 -3 -1 -2 -1 -4 
+H -2  0  1 -1 -3  0  0 -2  8 -3 -3 -1 -2 -1 -2 -1 -2 -2  2 -3  0  0 -1 -4 
+I -1 -3 -3 -3 -1 -3 -3 -4 -3  4  2 -3  1  0 -3 -2 -1 -3 -1  3 -3 -3 -1 -4 
+L -1 -2 -3 -4 -1 -2 -3 -4 -3  2  4 -2  2  0 -3 -2 -1 -2 -1  1 -4 -3 -1 -4 
+K -1  2  0 -1 -3  1  1 -2 -1 -3 -2  5 -1 -3 -1  0 -1 -3 -2 -2  0  1 -1 -4 
+M -1 -1 -2 -3 -1  0 -2 -3 -2  1  2 -1  5  0 -2 -1 -1 -1 -1  1 -3 -1 -1 -4 
+F -2 -3 -3 -3 -2 -3 -3 -3 -1  0  0 -3  0  6 -4 -2 -2  1  3 -1 -3 -3 -1 -4 
+P -1 -2 -2 -1 -3 -1 -1 -2 -2 -3 -3 -1 -2 -4  7 -1 -1 -4 -3 -2 -2 -1 -2 -4 
+S  1 -1  1  0 -1  0  0  0 -1 -2 -2  0 -1 -2 -1  4  1 -3 -2 -2  0  0  0 -4 
+T  0 -1  0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -2 -1  1  5 -2 -2  0 -1 -1  0 -4 
+W -3 -3 -4 -4 -2 -2 -3 -2 -2 -3 -2 -3 -1  1 -4 -3 -2 11  2 -3 -4 -3 -2 -4 
+Y -2 -2 -2 -3 -2 -1 -2 -3  2 -1 -1 -2 -1  3 -3 -2 -2  2  7 -1 -3 -2 -1 -4 
+V  0 -3 -3 -3 -1 -2 -2 -3 -3  3  1 -2  1 -1 -2 -2  0 -3 -1  4 -3 -2 -1 -4 
+B -2 -1  3  4 -3  0  1 -1  0 -3 -4  0 -3 -3 -2  0 -1 -4 -3 -3  4  1 -1 -4 
+Z -1  0  0  1 -3  3  4 -2  0 -3 -3  1 -1 -3 -1  0 -1 -3 -2 -2  1  4 -1 -4 
+X  0 -1 -1 -1 -2 -1 -1 -1 -1 -1 -1 -1 -1 -1 -2  0  0 -2 -1 -1 -1 -1 -1 -4 
+* -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4  1 
diff --git a/Binaries/x86-Binaries/Blast/blastall b/Binaries/x86-Binaries/Blast/blastall
diff --git a/Binaries/x86-Binaries/Ce/CE b/Binaries/x86-Binaries/Ce/CE
diff --git a/Binaries/x86-Binaries/Ce/pom/mkDB b/Binaries/x86-Binaries/Ce/pom/mkDB
diff --git a/Binaries/x86-Binaries/Ce/pom/mkDB_sgi b/Binaries/x86-Binaries/Ce/pom/mkDB_sgi
diff --git a/Binaries/x86-Binaries/Ce/pom/mkDB_sun b/Binaries/x86-Binaries/Ce/pom/mkDB_sun
diff --git a/Binaries/x86-Binaries/Clustalw/clustalw b/Binaries/x86-Binaries/Clustalw/clustalw
diff --git a/Binaries/x86-Binaries/Clustalw/clustalw-smp b/Binaries/x86-Binaries/Clustalw/clustalw-smp
diff --git a/Binaries/x86-Binaries/Fasta/fasta34_t b/Binaries/x86-Binaries/Fasta/fasta34_t
diff --git a/Binaries/x86-Binaries/Fasta/ssearch34_t b/Binaries/x86-Binaries/Fasta/ssearch34_t
diff --git a/Binaries/x86-Binaries/Glimmer/build-icm b/Binaries/x86-Binaries/Glimmer/build-icm
diff --git a/Binaries/x86-Binaries/Glimmer/extract b/Binaries/x86-Binaries/Glimmer/extract
diff --git a/Binaries/x86-Binaries/Glimmer/get-putative b/Binaries/x86-Binaries/Glimmer/get-putative
diff --git a/Binaries/x86-Binaries/Glimmer/glimmer.icm b/Binaries/x86-Binaries/Glimmer/glimmer.icm
diff --git a/Binaries/x86-Binaries/Glimmer/glimmer2 b/Binaries/x86-Binaries/Glimmer/glimmer2
diff --git a/Binaries/x86-Binaries/Glimmer/long-orfs b/Binaries/x86-Binaries/Glimmer/long-orfs
diff --git a/Binaries/x86-Binaries/Glimmer/run-glimmer2 b/Binaries/x86-Binaries/Glimmer/run-glimmer2
@@ -0,0 +1,16 @@
+echo "run Glimmer2"
+clear
+echo "Genome is " $1
+echo "Find non-overlapping orfs in  tmp.coord"
+rm -f tmp.coord
+./long-orfs $1 | ./get-putative >tmp.coord
+echo "Extract training sequences to  tmp.train"
+rm -f tmp.train
+./extract $1 tmp.coord >tmp.train
+wc tmp.train
+echo "Build interpolated context model in  tmp.model"
+rm -f tmp.model
+./build-icm <tmp.train >tmp.model
+echo "Predict genes with Glimmer2 with coordinates in  g2.coord"
+rm -f g2.coord
+./glimmer2 $1 tmp.model | ./get-putative >g2.coord
diff --git a/Binaries/x86-Binaries/Grappa/grappa b/Binaries/x86-Binaries/Grappa/grappa
diff --git a/Binaries/x86-Binaries/Hmmer/hmmpfam b/Binaries/x86-Binaries/Hmmer/hmmpfam
diff --git a/Binaries/x86-Binaries/Hmmer/hmmsearch b/Binaries/x86-Binaries/Hmmer/hmmsearch
diff --git a/Binaries/x86-Binaries/Phylip/dnapenny b/Binaries/x86-Binaries/Phylip/dnapenny