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Commits on Mar 8, 2012

• added sanity check to Alignments, throws IllegalArgumentException if compound sets mismatch (instead of just failing silently)

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Commits on Feb 24, 2012

• unified indentation in pom.xml; added some Test cases for DNA Alignments

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  brandstaetter

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Commits on Oct 6, 2011

• new unit test for DNA alignments

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  andreasprlic

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Commits on Oct 5, 2011

• adding a unit test that aligns a DNA sequence

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• Added missing intra-package import (Thanks to Hannes Brandstätter-Müller)

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Commits on Jul 6, 2011

• Contributing new framework for loading amino acid substitution matrices from the AAINDEX database.

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  andreasprlic

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Commits on Nov 2, 2010

• Modified in line with latest version of biojava3-core's Sequence interface

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Commits on Sep 28, 2010

• extending junit tests with conversion info

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Commits on Aug 20, 2010

• finished with linear space (anchored) alignments

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  markchapman

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Commits on Aug 12, 2010

• added alignment output formatting; outputs to CLUSTALW's ALN, FASTA, and GCG's MSF formats

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Commits on Aug 11, 2010

• refactored alignment routines: granted access to all score matrices, reduced memory requirement

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  markchapman

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Commits on Jul 29, 2010

• refactored aligner, scorer, and refiner enum types

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  markchapman

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Commits on Jul 28, 2010

• improvements to memory usage during multiple sequence alignment

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  markchapman

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• improvements to memory usage during multiple sequence alignment

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Commits on Jul 27, 2010

• cookbook programs

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  markchapman

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• updated tests to use SubstitutionMatrixHelper

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  markchapman

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Commits on Jul 22, 2010

• refactored AlignedSequence to have a Sequence generic type in addition to a Compound generic type

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  markchapman

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Commits on Jul 10, 2010

• added concurrent progressive multiple sequence alignment

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  markchapman

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Commits on Jul 9, 2010

• added caching of profile vectors

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  markchapman

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• refactored and commented GuideTree and GuideTreeNode, added Iterator from leaves to root

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  markchapman

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Commits on Jul 7, 2010

• implemented GuideTree as wrapper for forester's Phylogeny

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  markchapman

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• implemented profile-profile alignment

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  markchapman

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Commits on Jun 30, 2010

• tests for alternate scorers

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• minor: use String.format("%n") for line separator

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  markchapman

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Commits on Jun 29, 2010

• tests for profile-profile alignment data structure

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  markchapman

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• tests for local alignment and improved max and min alignment scores

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  markchapman

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• fixed tests in maven

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  markchapman

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• minor: performance improvements from FindBugs

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  markchapman

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• tests, 1 bug fix, and minor updates

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  markchapman

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Commits on Jun 21, 2010

• Location refactoring

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  markchapman

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Commits on Jun 19, 2010

• test files

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  markchapman

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Commits on Jun 17, 2010

• tests

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  markchapman

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• simplified defaults (loads blosum62)

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  markchapman

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• simplified defaults

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  markchapman

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Commits on Jun 16, 2010

• tests

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