Commit 4f7f0eac authored by Steffen Möller's avatar Steffen Möller
Browse files

New upstream version 14.1

parent 553cc3fa

README

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@@ -14,8 +14,9 @@ 
#               version 12.2       September 9, 2009              #

#               version 13.0       July 26, 2010                  #

#               version 14.0       December 2, 2011               #

#               version 14.1       October 17, 2017               #

#                                                                 #

#               Mikita Suyama (mikita@genome.med.kyoto-u.ac.jp)   #

#               Mikita Suyama (mikita@bioreg.kyushu-u.ac.jp)      #

#                                                                 #

#=================================================================#
@@ -35,6 +36,9 @@ The resulting codon-based DNA alignment can further be subjected 
to the calculation of synonymous (Ks) and non-synonymous (Ka)

substitution rates.



The script is licensed under GPL v2.







#-----------#

# Reference
@@ -176,7 +180,7 @@ Example: 


http://www.bork.embl.de/pal2nal

 or

http://www.genome.med.kyoto-u.ac.jp/cgi-bin/suyama/pal2nal/index.cgi

http://www.genome.med.kyoto-u.ac.jp/cgi-bin/suyama/pal2nal/index.cgi  (not working)





#---------#
@@ -186,10 +190,10 @@ http://www.genome.med.kyoto-u.ac.jp/cgi-bin/suyama/pal2nal/index.cgi 
If you have any questions or comments, please email me:



  Mikita Suyama

  Center for Genomic Medicine,

  Graduate School of Medicine, Kyoto University,

  606-8501 Kyoto, JAPAN

  tel: +81 75 753 4383

  fax: +81 75 753 4382

  email: mikita@genome.med.kyoto-u.ac.jp

  Medical Institute of Bioregulation

  Kyushu University,

  812-8582 Fukuoka, JAPAN

  tel: +81 92 642 6384

  fax: +81 92 642 6562

  email: mikita@bioreg.kyushu-u.ac.jp

pal2nal.pl

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#!/usr/bin/perl

#    pal2nal.pl (c) 2017 Mikita Suyama <mikita@bioreg.kyushu-u.ac.jp>

#

#    pal2nal.pl  (v14)                                      Mikita Suyama

#    #----------------------------------------#

#      This script is licensed under GPL v2.0

#    #----------------------------------------#

#

#

#

#    pal2nal.pl  (v14.1)                                      Mikita Suyama

#

#    Usage:  pal2nal.pl  pep.aln  nuc.fasta  [nuc.fasta...]  [options]  >  output

#
@@ -56,6 +63,10 @@ 
#            NUC1   GCTTGTGATGAATTTGGTGCTCGTCATG--GGG---TTTTAA

#            NUC2   GCGGG-GACGACTGG---GCGTAGCAC---GGGGG-TTTTGA

#    

#

#  v14.1

#     - licensed under GPL v2.0

#                                                          2017/10/17

#  v14.

#     - NCBI GenBank codon table

#                1  Universal code