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igortrucarandraug
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Bio::Tools::CodonTable: add codon table 15 (#389)
The codon table 15 was removed in 7f52ed5 to address #256 (updating CodonTable for current version which added codon tables 26-31 and removed codon table 15). However, it seems that codon table was added back to NCBI. This commit adds codon table #15 again.
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@@ -6,13 +6,14 @@ Summary of important user-visible changes for BioPerl
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using SUPER::new() [#307].
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* Fix test for BSML SAX by using lax parser XML::SAX::PurePerl since
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the external DTD URL now 404s [#376].
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* Added codon table 15 Bio::Tools::CodonTable [#389].
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1.7.8 2021-02-02 23:02:18-06:00 America/Chicago
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* Bio::SeqIO::interpro has been moved to a separate repository to
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deal with issues with XML::DOM::XPath bitrot [#347]
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* Pull requests:
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* Adjust Swiss-Prot FT A..B lines [#348] from @smoe
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* Update %FTQUAL_NO_QUOTE: List of qualifiers without quote [#339] from
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* Update %FTQUAL_NO_QUOTE: List of qualifiers without quote [#339] from
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@hdevillers
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1.7.7 2019-12-07 13:41:36-06:00 America/Chicago
@@ -27,7 +28,7 @@ Summary of important user-visible changes for BioPerl
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and a 'private' _sleep() function that mirror those from
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Bio::DB::WebDBSeqI, primarily for compliance with potential website
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restrictions for the number and frequency of queries (e.g. NCBI eUtils).
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* Fix bug #329, related to Bio::Tree::Statistics::transfer_bootstrap_expectation
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in last release.
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lib/Bio/Tools/CodonTable.pm

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@@ -215,7 +215,7 @@ BEGIN {
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'Alternative Yeast Nuclear',# 12
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'Ascidian Mitochondrial',# 13
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'Alternative Flatworm Mitochondrial',# 14
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'',
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'Blepharisma Nuclear',#15
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'Chlorophycean Mitochondrial',# 16
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'', '', '', '',
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'Trematode Mitochondrial',# 21
@@ -247,7 +247,7 @@ BEGIN {
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FFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
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FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGG
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FFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG
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''
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FFLLSSSSYY*QCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
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FFLLSSSSYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
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'' '' '' ''
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FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGG
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----------**--*----M---------------M----------------------------
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---M------**----------------------MM---------------M------------
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-----------*-----------------------M----------------------------
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''
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---M------**--*----M------------MMMM---------------M------------
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----------*---*--------------------M----------------------------
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'' '' '' ''
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----------**-----------------------M---------------M------------

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