updated scripts to 2025

eead-csic-compbio · Jan 8, 2025 · 2791e1a · 2791e1a
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diff --git a/CHANGES.txt b/CHANGES.txt
@@ -430,3 +430,4 @@
 14112024: fixed BLASTP check in install.pl
 14112024: updated release.pl
 14112024: moved Continuous Integration to Github action
+08012025: updated scripts to 2025, fixed ncbi-blast version in manuals
diff --git a/_split_blast.pl b/_split_blast.pl
@@ -1,6 +1,6 @@
 #!/usr/bin/env perl
 
-# 2013-20 Bruno Contreras
+# 2013-25 Bruno Contreras
 # Script to take advantage of multicore machines when running BLAST,
 # which seems to scale up to the number of physical cores in our tests.
 # Supports old BLAST (blastall) and new BLAST+ binaries.

diff --git a/_split_hmmscan.pl b/_split_hmmscan.pl
@@ -1,6 +1,6 @@
 #!/usr/bin/env perl
 
-# 2013-2020 Bruno Contreras, Pablo Vinuesa
+# 2013-2025 Bruno Contreras, Pablo Vinuesa
 # Script to take advantage of multicore machines when running hmmer3,
 # which seems to scale up to the number of physical cores in our tests.
 

diff --git a/add_pancore_matrices.pl b/add_pancore_matrices.pl
@@ -1,7 +1,7 @@
 #!/usr/bin/env perl
 
-# 2012-8 Bruno Contreras-Moreira (1) and Pablo Vinuesa (2):
-# 1: http://www.eead.csic.es/compbio (Estacion Experimental Aula Dei/CSIC/Fundacion ARAID, Spain)
+# 2012-2025 Bruno Contreras-Moreira (1) and Pablo Vinuesa (2):
+# 1: https://www.eead.csic.es/compbio (Estacion Experimental Aula Dei-CSIC/Fundacion ARAID, Spain)
 # 2: http://www.ccg.unam.mx/~vinuesa (Center for Genomic Sciences, UNAM, Mexico)
 
 # This script can be used to add pan/core data from .tab files generated by get_homologues.pl -c ,

diff --git a/add_pangenome_matrices.pl b/add_pangenome_matrices.pl
@@ -1,7 +1,7 @@
 #!/usr/bin/env perl
 
-# 2012 Bruno Contreras-Moreira (1) and Pablo Vinuesa (2):
-# 1: http://www.eead.csic.es/compbio (Estacion Experimental Aula Dei/CSIC/Fundacion ARAID, Spain)
+# 2012-2025 Bruno Contreras-Moreira (1) and Pablo Vinuesa (2):
+# 1: https://www.eead.csic.es/compbio (Estacion Experimental Aula Dei-CSIC/Fundacion ARAID, Spain)
 # 2: http://www.ccg.unam.mx/~vinuesa (Center for Genomic Sciences, UNAM, Mexico)
 
 # This script can be used to add pangenome matrices (-m files) generated by compare_clusters.pl,

diff --git a/annotate_cluster.pl b/annotate_cluster.pl
@@ -1,7 +1,7 @@
 #!/usr/bin/env perl
 
-# 2016-23 Bruno Contreras-Moreira (1), Ruben Sancho (1,2) and Pablo Vinuesa (3):
-# 1: http://www.eead.csic.es/compbio (Estacion Experimental Aula Dei-CSIC/Fundacion ARAID, Spain)
+# 2016-25 Bruno Contreras-Moreira (1), Ruben Sancho (1,2) and Pablo Vinuesa (3):
+# 1: httpa://www.eead.csic.es/compbio (Estacion Experimental Aula Dei-CSIC/Fundacion ARAID, Spain)
 # 2: Grupo Bioflora, EPS, Universidad de Zaragoza, Spain
 # 3: http://www.ccg.unam.mx/~vinuesa (Center for Genomic Sciences, UNAM, Mexico)
 

diff --git a/check_BDBHs.pl b/check_BDBHs.pl
@@ -1,7 +1,7 @@
 #!/usr/bin/env perl
 
-# 2013-23 Bruno Contreras-Moreira (1) and Pablo Vinuesa (2):
-# 1: https://www.eead.csic.es/compbio (Laboratory of Computational Biology, EEAD/CSIC, Spain)
+# 2013-25 Bruno Contreras-Moreira (1) and Pablo Vinuesa (2):
+# 1: https://www.eead.csic.es/compbio (Laboratory of Computational Biology, EEAD-CSIC, Spain)
 # 2: http://www.ccg.unam.mx/~vinuesa (Center for Genomic Sciences, UNAM, Mexico)
 
 # This script can be used to retrieve BLAST (bidirectional) best hits produced by get_homologues.pl and get_homologues-est.pl

diff --git a/compare_clusters.pl b/compare_clusters.pl
@@ -1,7 +1,7 @@
 #!/usr/bin/env perl
 
-# 2013-23 Bruno Contreras-Moreira (1) and Pablo Vinuesa (2):
-# 1: http://www.eead.csic.es/compbio (Laboratory of Computational Biology, EEAD-CSIC/Fundacion ARAID, Spain)
+# 2013-25 Bruno Contreras-Moreira (1) and Pablo Vinuesa (2):
+# 1: https://www.eead.csic.es/compbio (Laboratory of Computational Biology, EEAD-CSIC/Fundacion ARAID, Spain)
 # 2: http://www.ccg.unam.mx/~vinuesa (Center for Genomic Sciences, UNAM, Mexico)
 #
 # This script was originally written to compute the intersection between cluster lists produced

diff --git a/download_genomes_ncbi.pl b/download_genomes_ncbi.pl
@@ -1,6 +1,6 @@
 #!/usr/bin/env perl
 
-# 2013-20 Bruno Contreras-Moreira, Pablo Vinuesa
+# 2013-25 Bruno Contreras-Moreira, Pablo Vinuesa
 # download_genomes_ncbi.pl
 
 # Attempts to download a list of genomes from the NCBI.

diff --git a/get_homologues-est.pl b/get_homologues-est.pl
@@ -1,6 +1,6 @@
 #!/usr/bin/env perl 
 
-# 2015-2024 Bruno Contreras-Moreira (1) and Pablo Vinuesa (2):
+# 2015-2025 Bruno Contreras-Moreira (1) and Pablo Vinuesa (2):
 # 1: http://www.eead.csic.es/compbio (Estacion Experimental Aula Dei-CSIC/Fundacion ARAID, Spain)
 # 2: http://www.ccg.unam.mx/~vinuesa (Center for Genomic Sciences, UNAM, Mexico)
 

diff --git a/get_homologues.pl b/get_homologues.pl
@@ -1,7 +1,7 @@
 #!/usr/bin/env perl 
 
-# 2013-2024 Bruno Contreras-Moreira (1) and Pablo Vinuesa (2):
-# 1: http://www.eead.csic.es/compbio (Estacion Experimental Aula Dei-CSIC/Fundacion ARAID, Spain)
+# 2013-2025 Bruno Contreras-Moreira (1) and Pablo Vinuesa (2):
+# 1: https://www.eead.csic.es/compbio (Estacion Experimental Aula Dei-CSIC/Fundacion ARAID, Spain)
 # 2: http://www.ccg.unam.mx/~vinuesa (Center for Genomic Sciences, UNAM, Mexico)
 
 # This program uses BLAST (and DIAMOND/HMMER/Pfam) to define clusters of 'orthologous' ORF/intergenic

diff --git a/lib/HPCluster.pm b/lib/HPCluster.pm
@@ -6,7 +6,7 @@ package HPCluster;
 # but it should not be too dificult to add support for other systems (help welcome)
 
 # Bruno Contreras-Moreira, Pablo Vinuesa
-# 2020 CCG/UNAM, Mexico, EEAD/CSIC, Zaragoza, Spain
+# 2020-2025 CCG/UNAM, Mexico, EEAD/CSIC, Zaragoza, Spain
 
 use strict;
 require Exporter;

diff --git a/lib/marfil_homology.pm b/lib/marfil_homology.pm
@@ -2,7 +2,7 @@ package marfil_homology;
 
 # version 2.1
 
-# Code library created by Bruno Contreras-Moreira and Pablo Vinuesa (2006-2020)
+# Code library created by Bruno Contreras-Moreira and Pablo Vinuesa (2006-2025)
 # mainly for get_homologues.pl and get_homologues-est.pl
 
 # Contains code originally part of the following software:

diff --git a/lib/phyTools.pm b/lib/phyTools.pm
@@ -1,5 +1,5 @@
 # Bruno Contreras-Moreira, Pablo Vinuesa
-# 2005-24 CCG/UNAM, Mexico, EEAD/CSIC, Zaragoza, Spain
+# 2005-25 CCG-UNAM, Mexico, EEAD-CSIC, Zaragoza, Spain
 # This is a collection of subroutines used in our projects,
 # including primers4clades and get_homologues
 

diff --git a/make_nr_pangenome_matrix.pl b/make_nr_pangenome_matrix.pl
@@ -1,7 +1,7 @@
 #!/usr/bin/env perl
 
-# 2017-22 Bruno Contreras-Moreira (1) and Pablo Vinuesa (2):
-# 1: http://www.eead.csic.es/compbio (Laboratory of Computational Biology, EEAD/CSIC/Fundacion ARAID, Spain)
+# 2017-25 Bruno Contreras-Moreira (1) and Pablo Vinuesa (2):
+# 1: https://www.eead.csic.es/compbio (Laboratory of Computational Biology, EEAD-CSIC/Fundacion ARAID, Spain)
 # 2: http://www.ccg.unam.mx/~vinuesa (Center for Genomic Sciences, UNAM, Mexico)
 
 # This script computes a non-redundant pangenome matrix by comparing clusters with BLAST

diff --git a/manual_get_homologues-est.pdf b/manual_get_homologues-est.pdf
diff --git a/manual_get_homologues.pdf b/manual_get_homologues.pdf
diff --git a/parse_pangenome_matrix.pl b/parse_pangenome_matrix.pl
@@ -1,7 +1,7 @@
 #!/usr/bin/env perl
 
-# 2017-23 Bruno Contreras-Moreira (1) and Pablo Vinuesa (2):
-# 1: http://www.eead.csic.es/compbio (Estacion Experimental Aula Dei/CSIC/Fundacion ARAID, Spain)
+# 2017-25 Bruno Contreras-Moreira (1) and Pablo Vinuesa (2):
+# 1: https://www.eead.csic.es/compbio (Estacion Experimental Aula Dei-CSIC/Fundacion ARAID, Spain)
 # 2: http://www.ccg.unam.mx/~vinuesa (Center for Genomic Sciences, UNAM, Mexico)
 
 # This script can be used to get user-defined subsets of pangenome matrices generated by compare_clusters.pl

diff --git a/pfam_enrich.pl b/pfam_enrich.pl
@@ -1,7 +1,7 @@
 #!/usr/bin/env perl
 
-# 2016-21 Carlos P Cantalapiedra (1), Bruno Contreras-Moreira (1) and Pablo Vinuesa (2):
-# 1: http://www.eead.csic.es/compbio (Laboratory of Computational Biology, EEAD/CSIC, Spain)
+# 2016-25 Carlos P Cantalapiedra (1), Bruno Contreras-Moreira (1) and Pablo Vinuesa (2):
+# 1: https://www.eead.csic.es/compbio (Laboratory of Computational Biology, EEAD-CSIC, Spain)
 # 2: http://www.ccg.unam.mx/~vinuesa (Center for Genomic Sciences, UNAM, Mexico)
 
 # This script checks whether selected input clusters, produced by get_homologues.pl or 

diff --git a/plot_pancore_matrix.pl b/plot_pancore_matrix.pl
@@ -1,7 +1,7 @@
 #!/usr/bin/env perl
 
-# 2014-21 Bruno Contreras-Moreira (1) and Pablo Vinuesa (2):
-# 1: http://www.eead.csic.es/compbio (Estacion Experimental Aula Dei/CSIC/Fundacion ARAID, Spain)
+# 2014-25 Bruno Contreras-Moreira (1) and Pablo Vinuesa (2):
+# 1: https://www.eead.csic.es/compbio (Estacion Experimental Aula Dei-CSIC/Fundacion ARAID, Spain)
 # 2: http://www.ccg.unam.mx/~vinuesa (Center for Genomic Sciences, UNAM, Mexico)
 
 # This script can be used to plot pan/core charts from .tab files generated by get_homologues.pl -c