ER Thu Apr  9 11:48:47 EDT 2015

differences with erate-v.0.7 are:

fixed bug reported by Mira Han <mira.han@unlv.edu>,
regarding dnaml-erate seg faulting when using option U
that takes an input tree. Bug is fixed, and option U and option L
work now with dnml-erate.

souce code:
----------

easel             - Sequence analysis library (SRE unpublished). svn revision 293.

erate             - Generate evolved sequences using the generative model.

phylip3.66-erate  - Modified version of phylip3.66 package by Joe Felsenstein that includes the
                    the program dnamle. Added code: dnaml-erate.c, phylip-erate.c, phylip-erate.h,
                    seq-erate.c, seq-erate.h.

rose-1.3          - Modified version of program Rose (version 1.3)  by Stoye, Evers and Meyer.
                    Added functions have the ending "_er".



To create the executables:
-------------------------


rose
----
cd rose-1.3
autoconf
./configure
make
(executable is /rose-1.3/src/rose)

easel
----
cd easel
autoconf
./configure
make
(need the easel library to compile erate and phylip3.66-erate)

erate
-----
cd ../erate-generate/src
make
executables are:
  erate-generate - generates evolved sequences given a tree
  erate-tree     - generates a random tree using Kunher&Felsenstein algorithm


dnaml-erate
-----------
cd ../phylip3.66-erate/src
make all
  executable is dnaml-erate (in addition to all other phylip3.66 executables)


scripts
--------
to use some of the scripts you need to create the environmental variable ERATEDIR
for the path to erate-v.0.7
