Fix Versioning (now use bump-version.sh)
Use simplest ramxl until problems are resolved
name change for consistency
provisional raxml binaries for win/mac
provisional raxml binaries for win/mac
Merge branch 'release/1.1.0' of https://github.com/brettc/partitionfinder into release/1.1.0
Fix tests for windows

Need to quote command lines. And reduce the precision in the comparisons
updated raxml
updated manual

now we have strict clustering and relaxed clustering approaches
described properly.
Rename folder phyml to phylofiles
Put command line arguments into logfile
added brett's new version of RAxML

This version is compiled for x86 and i386. Hopefully it works on most
MACs. Thanks to brett for some nerdy wizadry to get this working.
cleaned out old RAxML versions
changed search methods to strict_clustering and relaxed_clustering

Right now some tests fail, for two different reasons.

1. It seems that having underscores in the .cfg file isn't allowed.
This is easy to fix (we can rename them again), but need to check if
there's a simple way to allow for underscores first.

2. We have a bug in our version of RAxML, in some cases we get this
error:

Assertion failed: (inputLikelihood == tr->likelihood), function modOpt,
file optimizeModel.c, line 3233.

I chatted with Alexis about this before. First we need to make 100%
sure we have the very latest version of RAxML. If we do, then we need
to get in touch with Alexis to see what the issue might be.

R
edited christoph's tests

to include the new algorithm names, and also simplified a couple so
that they run faster.
Keywords can now have hyphens and underscores
Spelling fixes to make tests run