initial commit

Author: sheneman

README

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+
+*****************************************************************************
+                       EVALYN -- EVolved ALYNments
+*****************************************************************************
+
+Copyright (C) 2006 Luke Sheneman
+
+A GA for iteratively refining guide trees by evolutionary
+computation for use in progressive multiple sequence alignment as 
+presented in:
+
+ Sheneman, L., J.A. Foster (2004) Evolving Better Multiple Sequence 
+ Alignments, Proceedings of the Genetic and Evolutionary Computation 
+ Conference (GECCO 2004), Seattle, WA.
+
+*****************************************************************************
+
+This version of EVALYN is not quite ready for public consumption.  I have 
+no useful help messages or documentation.  There is some critical missing
+functionality as well, such as the ability to properly handle ambiguity 
+codes in input sequences.  These will be added in future releases.
+
+Basically, EVALYN will read DNA or protein sequences in FASTA format
+and will output an alignment in Clustal W (*.ALN) format.  It will also output
+the best guide tree in Newick format.  Essentially, EVALYN maintains a 
+population of guide trees and iteratively evolves guide trees to improve 
+alignments as measured by a sum-of-pairs fitness function.
+
+
+TO BUILD EVALYN:
+----------------
+
+cd ./ltree
+make
+
+Executable is called "ltree", and will reside in the <evalyndist>/ltree 
+directory.
+
+
+EXAMPLE USAGE:
+--------------
+
+./ltree --infile=proteins.fasta --population=1000 --iterations=10000 \
+    --matrix=blosum62.txt --gapopen=-1.0 --gapextend=-0.1 --rnj
+
+Example substitution matrix formats are shown in <evalyndist>/ltree as:
+"def_dna_matrix.txt" and "def_pro_matrix.txt", which are also the 
+default substitution matrices if none are explicitly specified.
+
+
+COMMON COMMAND-LINE FLAGS:
+--------------------------
+
+** Inputs requiring arguments:
+
+ --infile   = <fasta-formatted input file>
+ --outfile  = <name of output file>
+ --treefile = <name of output Newick-formatted tree file>
+ --matrix   = <name of substitution matrix>
+ --population = <population size, ex. "--population = 500" >
+ --iterations = <number of iterations to run, ex. "--iterations = 1000">
+ --converge = <program stops when it converges when no improvement in x steps>
+ --mutation = <mutation rate, ex. "--mutation=0.01">
+ --gapopen = <cost of opening a gap region, ex. "--gapopen=-4.0">
+ --gapextend = <cost of extending a gap region, ex. "--gapextend=-1.0">
+ --seed = <the random number generated seedm ex, "--seed = 1000">
+
+
+
+** Inputs requiring NO arguments
+
+ --rnj     : seeds population with a relaxed neighbod joining tree>
+ --dna     : specifies that input is a DNA sequence
+ --protein : specifies that input is a protein sequence
+
+****************************************************************************
+
+Please direct questions to: 
+
+Luke Sheneman
+sheneman@cs.uidaho.edu
+
+University of Idaho
+
+****************************************************************************
+

lib/align/Makefile

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+#
+# Makefile for alignment library
+#
+# $Id: Makefile,v 1.1.1.1 2006/05/09 21:00:46 cvsuser Exp $
+#
+#
+# Copyright (c) 2003 Luke Sheneman.  All rights reserved.
+#
+# Luke Sheneman
+# sheneman@cs.uidaho.edu
+#
+#
+
+CC	= gcc
+CFLAGS = -O3 -g3 -Wall -funroll-loops -march=pentium4 -mcpu=pentium4 -ffast-math -fprefetch-loop-arrays -finline-limit=5000 -fomit-frame-pointer -msse2 -mmmx -fno-strict-aliasing
+#CFLAGS = -O3 -Wall -funroll-loops -march=pentium4 -mcpu=pentium4 -fno-unsafe-math-optimizations -fprefetch-loop-arrays -finline-limit=5000 -fomit-frame-pointer -fno-strict-aliasing
+#CFLAGS = -O3 -g3 -Wall -funroll-loops -finline-limit=5000 -fomit-frame-pointer -fno-strict-aliasing -fno-unsafe-math-optimizations
+#CFLAGS = -pg -Wall -fno-inline -fno-strict-aliasing
+#CFLAGS = -g3 -Wall -fno-strict-aliasing
+#CLINKER	= /usr/mpi-beowulf/bin/mpicc
+INCDIR  = ../prng
+LIBS	=	
+DEFS 	=
+
+SRCS    = align.c msf.c aln.c fasta.c submat.c syms.c symtab.c cache.c
+OBJS	= align.o msf.o aln.o fasta.o submat.o syms.o symtab.o cache.o
+
+
+all: align.a
+
+clean:
+	rm -f *.o a.out *.a libalign.a
+
+.c.o:
+	$(CC) -c $(CFLAGS) -I$(INCDIR) $(OPTFLAGS) $(DEFS) $<
+
+align.a: $(OBJS)
+	rm -f libalign.a
+	ar -rs libalign.a $(OBJS)
+
+