Fuzzy Multiple Sequence Alignment




File list:
Alignment_Prob-master
....................\alignCompress
....................\.............\C.version
....................\.............\.........\m-align
....................\.............\.........\.......\.cvsignore
....................\.............\.........\.......\common.c
....................\.............\.........\.......\common.h
....................\.............\.........\.......\COPYRIGHT
....................\.............\.........\.......\m-align.c
....................\.............\.........\.......\Makefile
....................\.............\.........\.......\markov.c
....................\.............\.........\.......\markov.h
....................\.............\.........\.......\markov_pred.c
....................\.............\.........\.......\README
....................\.............\.........\.cvsignore
....................\.............\.........\count_markov.pl
....................\.............\.........\extractPopData.pl
....................\.............\.........\main.c
....................\.............\.........\main.h
....................\.............\.........\Makefile
....................\.............\.........\markov.c
....................\.............\.........\Markov_gen.pm
....................\.............\.........\populationPlot.pl
....................\.............\.........\populationRun.pl
....................\.............\.........\unused.c
....................\.............\paper
....................\.............\.....\AI2004
....................\.............\.....\......\AI2004-submission.html
....................\.............\.....\......\AI2004.ps
....................\.............\.....\......\AI2004.tex
....................\.............\.....\......\AI2004.tex.bak
....................\.............\.....\......\AI2004.tgz
....................\.............\.....\......\history.txt
....................\.............\.....\......\llncs.cls
....................\.............\.....\......\llncs.dem
....................\.............\.....\......\llncs.doc
....................\.............\.....\......\llncs.dvi
....................\.............\.....\......\llncs.ind
....................\.............\.....\......\llncs2e.zip
....................\.............\.....\......\llncsdoc.sty
....................\.............\.....\......\Makefile
....................\.............\.....\......\read.me
....................\.............\.....\......\roc_blend.eps
....................\.............\.....\......\roc_uni_0.eps
....................\.............\.....\......\splncs.bst
....................\.............\.....\......\sprmindx.sty
....................\.............\.....\......\subjidx.ind
....................\.............\.....\3state.eps
....................\.............\.....\3state.fig
....................\.............\.....\acm_proc_article-sp.cls
....................\.............\.....\alignCompress.tex
....................\.............\.....\alternate.tex
....................\.............\.....\bioinformatics-submitted.txt
....................\.............\.....\bioinformatics2003-reject.txt
....................\.............\.....\bioinformatics2003.tex
....................\.............\.....\ismb2003-reject.txt
....................\.............\.....\ismb2003.tex
....................\.............\.....\local.eps
....................\.............\.....\local.fig
....................\.............\.....\Makefile
....................\.............\.....\PfEMP1.notes
....................\.............\.....\recomb2003.tex
....................\.............\.....\roc_0.eps
....................\.............\.....\roc_blend.eps
....................\.............\.....\roc_uni.eps
....................\.............\.....\roc_uni_0.eps
....................\.............\testRuns
....................\.............\........\blast_retrieve
....................\.............\........\..............\blast
....................\.............\........\..............\.....\.cvsignore
....................\.............\........\..............\.....\blast.hits.PfEMP1.filtered.10
....................\.............\........\..............\.....\blast.pl
....................\.............\........\..............\.....\get_seq.pl
....................\.............\........\..............\.....\t.pl
....................\.............\........\..............\.cvsignore
....................\.............\........\..............\hits_to_fasta.pl
....................\.............\........\..............\join_other_results.pl
....................\.............\........\..............\PfEMP1.bits.fa
....................\.............\........\..............\ranks.pl
....................\.............\........\..............\run_pairwise.pl
....................\.............\........\..............\set_cutoff.pl
....................\.............\........\frontend
....................\.............\........\........\frontend.py
....................\.............\........\........\gui.ui
....................\.............\........\test_mutate
....................\.............\........\...........\.cvsignore
....................\.............\........\...........\count.pl
....................\.............\........\...........\DPA.pm
....................\.............\........\...........\entropy.pl
....................\.............\........\...........\example1_related
....................\.............\........\...........\example1_unrelated
....................\.............\........\...........\logFileEntropy.pl
....................\.............\........\...........\Markov.pm
....................\.............\........\...........\Markov_gen.pm
....................\.............\........\...........\Multi_model.pm
....................\.............\........\...........\mutate.pl
....................\.............\........\...........\run_prss.pl
....................\.............\........\...........\run_ssearch.pl
....................\.............\........\...........\run_ssearch_modified.pl
....................\.............\........\...........\split2.pl
....................\.............\........\...........\UKK.pm
....................\.............\........\.cvsignore
....................\.............\........\check.pl
....................\.............\........\DPA.pm
....................\.............\........\extractData.pl
....................\.............\........\extractPopData.pl
....................\.............\........\Markov_gen.pm
....................\.............\........\Multi_model.pm
....................\.............\........\paramsPlot.pl
....................\.............\........\populationPlot.pl
....................\.............\........\populationPlot2.pl
....................\.............\........\populationRun.pl
....................\.............\........\populationRun2.pl
....................\.............\........\relatedPlot.pl
....................\.............\........\runAll.pl
....................\.............\........\testRun.pl
....................\.............\........\UKK.pm
....................\.............\AlignCompress.java
....................\.............\myManifest
....................\.............\NOTE
....................\common
....................\......\Alignment_viewer.java
....................\......\Buffered_Seq_Model.java
....................\......\CommandLine.java
....................\......\Counts.java
....................\......\DNA.java
....................\......\Has_Value.java
....................\......\MarkovN.java
....................\......\MarkovN_exact.java
....................\......\MarkovN_fitted.java
....................\......\Misc.java
....................\......\Model_SeqAB.java
....................\......\Multinomial.java
....................\......\Mutation_1State.java
....................\......\Mutation_3State.java
....................\......\Mutation_FSM.java
....................\......\MyMath.java
....................\......\Params.java
....................\......\Seq_Model.java
....................\......\Two_Seq_Model.java
....................\......\Two_Seq_Model_Counts.java
....................\fuzzyLZ
....................\.......\ExactMatches.java
....................\.......\FuzzyDriver.java
....................\.......\FuzzyLZ.java
....................\.......\FuzzyLZ_FSM.fig
....................\.......\Matches_Sparse.java
....................\.......\Model_SeqA.java
....................\.......\Model_SeqA_SubModel.java
....................\.......\myManifest
....................\.......\Plot.java
....................\.......\Sparse.java
....................\.cvsignore
....................\.gitignore
....................\COPYRIGHT
....................\fuzzyLZ-params.txt
....................\Makefile
....................\Makefile.fuzzyLZ
....................\NOTE.nucleotide_codes
....................\PfEMP1
....................\README.alignCompress
....................\README.FuzzyLZ
....................\README.md
....................\smooth.pl
....................\tar.pl