Remove Windows style new lines (suggested by @mgymrek)
Thank Melissa Gymrek for fastsimcoal work (GitHub #293)
fastsimcoal2 support (squashed commit from pull request #293)
Revert change which broke detecting simcaol2.exe on Windows
fixed cpairwise2 import issue under python3
Thank Chunlei Wu for cpairwise2 fix
SimCoal test removal
Simcoal deprecation
Simcoal deprecation
Explicit error from failed SFF assert in _check_eof
Add missing print-and-compare output for test_Fasttree_tool.py

Generated using FastTree 2.1.7 SSE3 on 64bit Linux.
Windows file system case insensitive; actually try docuemented path
Remove unused variable
FastTree website does not use fasttree (lower case) for binary
Use the -nt switch in FastTree test

Using a self compiled copy of the latest source code from the
website under Mac OS X, this fails:

```
$ FastTree Quality/example.fasta
FastTree Version 2.1.7 SSE3
Alignment: Quality/example.fasta
Amino acid distances: BLOSUM45 Joins: balanced Support: SH-like 1000
Search: Normal +NNI +SPR (2 rounds range 10) +ML-NNI opt-each=1
TopHits: 1.00*sqrtN close=default refresh=0.80
ML Model: Jones-Taylor-Thorton, CAT approximation with 20 rate categories
WARNING! 100.0% NUCLEOTIDE CHARACTERS -- IS THIS REALLY A PROTEIN ALIGNMENT?
Segmentation fault: 11
```

With the -nt switch:

```
$ FastTree -nt Quality/example.fasta
FastTree Version 2.1.7 SSE3
Alignment: Quality/example.fasta
Nucleotide distances: Jukes-Cantor Joins: balanced Support: SH-like 1000
Search: Normal +NNI +SPR (2 rounds range 10) +ML-NNI opt-each=1
TopHits: 1.00*sqrtN close=default refresh=0.80
ML Model: Jukes-Cantor, CAT approximation with 20 rate categories
Initial topology in 0.00 seconds
Refining topology: 6 rounds ME-NNIs, 2 rounds ME-SPRs, 3 rounds ML-NNIs
Total branch-length 4.207 after 0.00 sec
ML-NNI round 1: LogLk = -103.915 NNIs 0 max delta 0.00 Time 0.00
Switched to using 20 rate categories (CAT approximation)
Rate categories were divided by 0.742 so that average rate = 1.0
CAT-based log-likelihoods may not be comparable across runs
Use -gamma for approximate but comparable Gamma(20) log-likelihoods
ML-NNI round 2: LogLk = -102.022 NNIs 0 max delta 0.00 Time 0.00
Turning off heuristics for final round of ML NNIs (converged)
ML-NNI round 3: LogLk = -102.022 NNIs 0 max delta 0.00 Time 0.00 (final)
Optimize all lengths: LogLk = -101.474 Time 0.00
Total time: 0.00 seconds Unique: 3/3 Bad splits: 0/0
(EAS54_6_R1_2_1_413_324:5.99294,EAS54_6_R1_2_1_540_792:0.40690,EAS54_6_R1_2_1_443_348:1.20540);
```

However, using the provided binary for 64 bit Linux, -nt is not needed
to avoid the crash:

```
$ FastTree Quality/example.fasta
FastTree Version 2.1.7 SSE3
Alignment: Quality/example.fasta
Amino acid distances: BLOSUM45 Joins: balanced Support: SH-like 1000
Search: Normal +NNI +SPR (2 rounds range 10) +ML-NNI opt-each=1
TopHits: 1.00*sqrtN close=default refresh=0.80
ML Model: Jones-Taylor-Thorton, CAT approximation with 20 rate categories
WARNING! 100.0% NUCLEOTIDE CHARACTERS -- IS THIS REALLY A PROTEIN ALIGNMENT?
Initial topology in 0.00 seconds
Refining topology: 6 rounds ME-NNIs, 2 rounds ME-SPRs, 3 rounds ML-NNIs
Total branch-length 3.999 after 0.00 sec
ML-NNI round 1: LogLk = -215.248 NNIs 0 max delta 0.00 Time 0.00
Switched to using 20 rate categories (CAT approximation)
Rate categories were divided by 0.743 so that average rate = 1.0
CAT-based log-likelihoods may not be comparable across runs
Use -gamma for approximate but comparable Gamma(20) log-likelihoods
ML-NNI round 2: LogLk = -213.456 NNIs 0 max delta 0.00 Time 0.00
Turning off heuristics for final round of ML NNIs (converged)
ML-NNI round 3: LogLk = -213.456 NNIs 0 max delta 0.00 Time 0.00 (final)
Optimize all lengths: LogLk = -213.359 Time 0.00
Total time: 0.01 seconds Unique: 3/3 Bad splits: 0/0
(EAS54_6_R1_2_1_413_324:3.43961,EAS54_6_R1_2_1_540_792:0.47246,EAS54_6_R1_2_1_443_348:1.44117);
```

However, since the examples are actually nucleotides best to use it
and not treat things as protein:

```
$ FastTree -nt  Quality/example.fasta
FastTree Version 2.1.7 SSE3
Alignment: Quality/example.fasta
Nucleotide distances: Jukes-Cantor Joins: balanced Support: SH-like 1000
Search: Normal +NNI +SPR (2 rounds range 10) +ML-NNI opt-each=1
TopHits: 1.00*sqrtN close=default refresh=0.80
ML Model: Jukes-Cantor, CAT approximation with 20 rate categories
Initial topology in 0.00 seconds
Refining topology: 6 rounds ME-NNIs, 2 rounds ME-SPRs, 3 rounds ML-NNIs
Total branch-length 4.207 after 0.00 sec
ML-NNI round 1: LogLk = -103.915 NNIs 0 max delta 0.00 Time 0.00
Switched to using 20 rate categories (CAT approximation)
Rate categories were divided by 0.742 so that average rate = 1.0
CAT-based log-likelihoods may not be comparable across runs
Use -gamma for approximate but comparable Gamma(20) log-likelihoods
ML-NNI round 2: LogLk = -102.022 NNIs 0 max delta 0.00 Time 0.00
Turning off heuristics for final round of ML NNIs (converged)
ML-NNI round 3: LogLk = -102.022 NNIs 0 max delta 0.00 Time 0.00 (final)
Optimize all lengths: LogLk = -101.474 Time 0.00
Total time: 0.00 seconds Unique: 3/3 Bad splits: 0/0
(EAS54_6_R1_2_1_413_324:5.99294,EAS54_6_R1_2_1_540_792:0.40690,EAS54_6_R1_2_1_443_348:1.20540);
``

Notice the very different branch lengths!
Update FastaIO.py

Fix typo.
simcoal -> fastsimcoal
wMerge branch 'master' of github.com:biopython/biopython
Update exonerate parser to handle dna2protein model
Display similarity character in HSPs only when it's a string