List of files in the package.
----------------------------

Manual.ps    -- decription of program, run options & demo examples
                (postscript format)
MANUAL       -- decription of program, run options & demo examples
                (text format)
INSTALL      -- instructions for installing the programs
COPYING      -- copyright notice, and information on distribution policy
FILES        -- overview of what files are (this file)
GNULICENSE   -- Gnu Public License, version 2 (see COPYING)
Release.history -- Log of changes/fixes/additions in various releases 
          
Makefile         -- Customize local installation
checkversion.pl  -- Makes sure you are using Perl version 5.0 or greater 
                    when 'make'ing tRNAscan-SE
instman.pl       -- PERL script used for man page installation
tRNAscan-SE.man  -- Manual file for tRNAscan-SE

Files created after a complete 'make':

tRNAscan-SE          ready-to-run PERL script, user runs this program to
                     search for tRNAs
covels-SE            copy of 'covels' program from Cove package, 
                     renamed with '-SE' suffix to avoid overwriting
                     previous installation of Cove package
coves-SE             copy of 'coves' program from Cove package, 
                     renamed with '-SE' suffix to avoid overwriting
                     previous installation of Cove package
trnascan-1.4         optimized, debugged version of tRNAscan 1.3 with
                     a couple new options for use with tRNAscan-SE             
eufindtRNA           new implementation of tRNA-finding algorithm 
                     previously described by Pavesi et al.;
                     does step-wise identification of B box, then A
                     box, then poly-T termination signal, scored with
                     newly derived log odds score matrix; new options
                     included for use with tRNAscan-SE

Source / data files for tRNAscan-SE:

tRNAscan-SE.src      PERL script source, must be run thru a 'make' to
                     do variable substitutions and create executable
                     file 'tRNAscan-SE'

gcode.cilnuc	     Alternate genetic codes for Ciliates,
                      Dasycladacean, & Hexamita nuclear tRNAs 
gcode.echdmito	     "  "  "  "    Echinoderm mitochondrial tRNAs
gcode.invmito        "  "  "  "    Invertibrate mitochondrial tRNAs
gcode.othmito        "  "  "  "    Mold, Protozoans, & Coelenterate 
                      mitochondrial tRNAs
gcode.vertmito       "  "  "  "    Vertibrate mitochondrial tRNAs
gcode.ystmito        "  "  "  "    Yeast mitochondrial tRNAs

sstofa.pl            PERL script utility program that converts a
		     tRNA secondary-structure file (-f option)
		     into a standard FASTA file; not required
		     for tRNAscan-SE operation, supplied as 
		     an external utility to user

Source / data files for tRNAscan program:

trnascan.c	     source for tRNAscan v.1.4 
Dsignal		     D arm consensus matrix scoring file 
TPCsignal            TPC arm consensus matrix scoring file


Source files for eufindtRNA program:

eufind_main.c        main source file
pavesi.c             tRNA feature search functions
eufind_const.h       constants & data structures


Source / data files for Cove package:

TRNA2.cm             default covariance model used by Cove to detect tRNAs
                     (built from hand-edited alignment of over 
                     1415 tRNAs, introns included, by S. Eddy)
TRNA2ns.cm           primary-structure only (HMM-like) covariance model used by
		     Cove to separate primary sequence scores from
		     secondary structure scores (see Methods);
                     this model uses the same tRNA alignment as
		     TRNA2.cm, but excludes all secondary structure
		     information

PSELC.cm	     covariance model used to detect prokaryotic
                     selenocysteine tRNAs (also gives more accurate 
		     secondary structure predictions of selcys tRNAs)
                     trained on 5 known prok selcys tRNAs
ESELC.cm             covariance model used to detect eukaryotic
	             selenocysteine tRNAs (also gives more accurate 
		     secondary structure predictions of selcys tRNAs)
		     trained on 7 known euk selcys tRNAs

align_main.c         main() for covea,  multiple alignment
build_main.c         main() for coveb,  model construction
emit_main.c          main() for covee,  emit sequences from a model
scan_main.c          main() for covels, database searching
score_main.c         main() for coves,  scoring sequences and predicting their structure
structcheck_main.c   main() for an auxiliary program that checks 
		     structure-annotated alignments
train_main.c         main() for covet,  model training

dbviterbi.c          database scanning version of the alignment algorithm
smallviterbi.c       small memory version of the alignment algorithm (EXPERIMENTAL)
viterbi.c            alignment algorithm

align.c              produce output alignments from tracebacks
debug.c              miscellaneous debugging output routines
emit.c               emit sequences from a model
fastmodelmaker.c     N^2 mem/N^3 time, approx. model construction from alignment
konings.c            secondary structure "strings"
maxmodelmaker.c      N^2 mem/N^4 time, max. likelihood model construction from alignment
misc.c               miscellaneous functions
model.c              alloc, init, free'ing of a CM
prior.c              default prior, i/o of prior from files
probify.c            convert counts to probabilities
save.c               i/o of models
scorestack.c         module for 
structs.c            implementation of data structures: trees & stacks
trace.c              trace tree & stack data structures


Files borrowed from Sean Eddy's sequence function library (v.1.5g & j):

alignio.c            i/o of aligned sequence files
sqerror.c            Die(), Choke(), Warn() error functions
sqio.c               Don Gilbert's readseq, i/o of sequences
getopt.c             More portable version of getopt()
iupac.c              values of global variables
msf.c                i/o of GCG MSF alignment format
revcomp.c            reverse complement a sequence
selex.c              i/o of my SELEX alignment format
sre_ctype.c          portability of ctype.h functions
sre_string.c         some miscellaneous extra string functions
types.c              some miscellaneous type-checking functions for user input
gnuregex.c           regular expression function library
interleaved.c        i/o of interleaved format multiple alignments 
reformat_main.c      source for useful sequence format conversion program
revcomp_main.c       source for program to take the reverse complement of
		     a sequence
seqstat_main.c       source for a program displaying information about
		     a sequence file
shuffle_main.c	     source for a program that shuffles input sequence
		     randomly, useful for running Monte Carlo simulations

Files in /Demo for running demo examples:

/Demo/C28G1.fa,      C. elegans cosmids
      F22B7.fa, 
      F59C12.fa

/Demo/Sprz-sub.fa    1014 sequence subset of Sprinzl tRNA 
                      (contains animal cytoplasmic + eubacterial tRNAs)
/Demo/DQ6060.fa      Sprinzl Tetrahymena thermophila Gln tRNA

Files in /Cove (additional files in Cove package not needed for 
                tRNAscan-SE operation):

/Cove/Guide.tex      User's Guide for Cove package, in TeX format
/Cove/DEMO           Running demo's of various programs in entire
                      Cove package
/Cove/Demos/*        Files needed for running Cove package demos
/Cove/COPYING        copyright notice for Cove package, and
                      information on distribution policy 
