 ../
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alignment/
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1140
(12 years ago)
by jmduarteg:
Fixed bug: now nucleotide alignment is in same order as protein alignment
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UniprotEntry.java
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1142
(12 years ago)
by jmduarteg:
Now nucleotide alignment contains reference sequence as well. Moved entropy and kaks calc methods to UniprotHomologList.
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UniprotHomologList.java
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1142
(12 years ago)
by jmduarteg:
Now nucleotide alignment contains reference sequence as well. Moved entropy and kaks calc methods to UniprotHomologList.
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Codon.java
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1136
(12 years ago)
by jmduarteg:
New ambiguous nucleotide w.
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GeneticCodeType.java
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1132
(12 years ago)
by jmduarteg:
New SelectonRunner class. More taxonomy information retrieved from uniprot.
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ProteinToCDSMatch.java
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1126
(12 years ago)
by jmduarteg:
New code to obtain the nucleotide alignment by mapping the aminoacid alignment to the nucleotide sequences.
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TranslatedFrame.java
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1122
(12 years ago)
by jmduarteg:
Some refactoring
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UniprotHomolog.java
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1120
(12 years ago)
by jmduarteg:
New class UniprotEntry. Things make a lot more sense now...
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Sequence.java
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1119
(12 years ago)
by jmduarteg:
Now checking also for ambiguous nucleotide codes (n, m) when translating. Changed implementation of translation by using the new Codon class.
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TranslationException.java
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1119
(12 years ago)
by jmduarteg:
Now checking also for ambiguous nucleotide codes (n, m) when translating. Changed implementation of translation by using the new Codon class.
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Translator.java
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1119
(12 years ago)
by jmduarteg:
Now checking also for ambiguous nucleotide codes (n, m) when translating. Changed implementation of translation by using the new Codon class.
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geneticCode.dat
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1114
(12 years ago)
by jmduarteg:
New feature: code for dna to protein translation
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ReadingFrame.java
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1114
(12 years ago)
by jmduarteg:
New feature: code for dna to protein translation
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