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Here is a list of all documented files with brief descriptions:
hmmer-2.1.2/Shiva/alignalign_test.c [code]
hmmer-2.1.2/Shiva/evd_test.c [code]
hmmer-2.1.2/Shiva/masks_test.c [code]
hmmer-2.1.2/Shiva/parsingviterbi_test.c [code]
hmmer-2.1.2/Shiva/tophits_test.c [code]
hmmer-2.1.2/Shiva/trace_test.c [code]
hmmer-2.1.2/Shiva/viterbi_exercise.c [code]
hmmer-2.1.2/Shiva/weeviterbi_test.c [code]
hmmer-2.1.2/src/aligneval.c [code]
hmmer-2.1.2/src/alignio.c [code]
hmmer-2.1.2/src/alistat_main.c [code]
hmmer-2.1.2/src/alphabet.c [code]
hmmer-2.1.2/src/cluster.c [code]
hmmer-2.1.2/src/config.h [code]
hmmer-2.1.2/src/core_algorithms.c [code]
hmmer-2.1.2/src/dayhoff.c [code]
hmmer-2.1.2/src/debug.c [code]
hmmer-2.1.2/src/emit.c [code]
hmmer-2.1.2/src/emulation.c [code]
hmmer-2.1.2/src/file.c [code]
hmmer-2.1.2/src/funcs.h [code]
hmmer-2.1.2/src/getopt.c [code]
hmmer-2.1.2/src/getseq_main.c [code]
hmmer-2.1.2/src/globals.h [code]
hmmer-2.1.2/src/gnuregex.h [code]
hmmer-2.1.2/src/gsi.c [code]
hmmer-2.1.2/src/histogram.c [code]
hmmer-2.1.2/src/hmmalign.c [code]
hmmer-2.1.2/src/hmmbuild.c [code]
hmmer-2.1.2/src/hmmcalibrate-pvm.c [code]
hmmer-2.1.2/src/hmmcalibrate.c [code]
hmmer-2.1.2/src/hmmconvert.c [code]
hmmer-2.1.2/src/hmmemit.c [code]
hmmer-2.1.2/src/hmmfetch.c [code]
hmmer-2.1.2/src/hmmindex.c [code]
hmmer-2.1.2/src/hmmio.c [code]
hmmer-2.1.2/src/hmmpfam-pvm.c [code]
hmmer-2.1.2/src/hmmpfam.c [code]
hmmer-2.1.2/src/hmmsearch-pvm.c [code]
hmmer-2.1.2/src/hmmsearch.c [code]
hmmer-2.1.2/src/hsregex.c [code]
hmmer-2.1.2/src/interleaved.c [code]
hmmer-2.1.2/src/iupac.c [code]
hmmer-2.1.2/src/masks.c [code]
hmmer-2.1.2/src/mathsupport.c [code]
hmmer-2.1.2/src/misc.c [code]
hmmer-2.1.2/src/modelmakers.c [code]
hmmer-2.1.2/src/msf.c [code]
hmmer-2.1.2/src/plan7.c [code]
hmmer-2.1.2/src/plan9.c [code]
hmmer-2.1.2/src/prior.c [code]
hmmer-2.1.2/src/pvm.c [code]
hmmer-2.1.2/src/revcomp.c [code]
hmmer-2.1.2/src/selex.c [code]
hmmer-2.1.2/src/seqstat_main.c [code]
hmmer-2.1.2/src/sqerror.c [code]
hmmer-2.1.2/src/sqfuncs.h [code]
hmmer-2.1.2/src/sqio.c [code]
hmmer-2.1.2/src/squid.h [code]
hmmer-2.1.2/src/sre_ctype.c [code]
hmmer-2.1.2/src/sre_math.c [code]
hmmer-2.1.2/src/sre_string.c [code]
hmmer-2.1.2/src/sreformat_main.c [code]
hmmer-2.1.2/src/stack.c [code]
hmmer-2.1.2/src/structs.h [code]
hmmer-2.1.2/src/threads.c [code]
hmmer-2.1.2/src/tophits.c [code]
hmmer-2.1.2/src/trace.c [code]
hmmer-2.1.2/src/translate.c [code]
hmmer-2.1.2/src/types.c [code]
hmmer-2.1.2/src/version.h [code]
hmmer-2.1.2/src/weight.c [code]

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