File list (Check if you may need any files):
Alignment_Prob-master
.....................\.cvsignore
.....................\.gitignore
.....................\COPYRIGHT
.....................\Makefile
.....................\Makefile.fuzzyLZ
.....................\NOTE.nucleotide_codes
.....................\PfEMP1
.....................\README.FuzzyLZ
.....................\README.alignCompress
.....................\README.md
.....................\alignCompress
.....................\.............\AlignCompress.java
.....................\.............\C.version
.....................\.............\.........\.cvsignore
.....................\.............\.........\Makefile
.....................\.............\.........\Markov_gen.pm
.....................\.............\.........\count_markov.pl
.....................\.............\.........\extractPopData.pl
.....................\.............\.........\m-align
.....................\.............\.........\.......\.cvsignore
.....................\.............\.........\.......\COPYRIGHT
.....................\.............\.........\.......\Makefile
.....................\.............\.........\.......\README
.....................\.............\.........\.......\common.c
.....................\.............\.........\.......\common.h
.....................\.............\.........\.......\m-align.c
.....................\.............\.........\.......\markov.c
.....................\.............\.........\.......\markov.h
.....................\.............\.........\.......\markov_pred.c
.....................\.............\.........\main.c
.....................\.............\.........\main.h
.....................\.............\.........\markov.c
.....................\.............\.........\populationPlot.pl
.....................\.............\.........\populationRun.pl
.....................\.............\.........\unused.c
.....................\.............\NOTE
.....................\.............\myManifest
.....................\.............\paper
.....................\.............\.....\3state.eps
.....................\.............\.....\3state.fig
.....................\.............\.....\AI2004
.....................\.............\.....\......\AI2004-submission.html
.....................\.............\.....\......\AI2004.ps
.....................\.............\.....\......\AI2004.tex
.....................\.............\.....\......\AI2004.tex.bak
.....................\.............\.....\......\AI2004.tgz
.....................\.............\.....\......\Makefile
.....................\.............\.....\......\history.txt
.....................\.............\.....\......\llncs.cls
.....................\.............\.....\......\llncs.dem
.....................\.............\.....\......\llncs.doc
.....................\.............\.....\......\llncs.dvi
.....................\.............\.....\......\llncs.ind
.....................\.............\.....\......\llncs2e.zip
.....................\.............\.....\......\llncsdoc.sty
.....................\.............\.....\......\read.me
.....................\.............\.....\......\roc_blend.eps
.....................\.............\.....\......\roc_uni_0.eps
.....................\.............\.....\......\splncs.bst
.....................\.............\.....\......\sprmindx.sty
.....................\.............\.....\......\subjidx.ind
.....................\.............\.....\Makefile
.....................\.............\.....\PfEMP1.notes
.....................\.............\.....\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
.....................\......