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
Fix bytes vs unicode error when missing DTD
Update Seq.py

Fix the docstring of Seq().count() and MutableSeq().count().
More updated NCBI DTD files.

Adding http://www.ncbi.nlm.nih.gov/corehtml/query/DTD/bookdoc_140101.dtd
and http://www.ncbi.nlm.nih.gov/corehtml/query/DTD/pubmed_140101.dtd
and http://www.ncbi.nlm.nih.gov/corehtml/query/DTD/nlmmedlinecitationset_140101.dtd

Reported by email.