Added useful variable initialization for Ellison (2007), making the
optimization much more stable.
update alignment code which now allows to add alignments as simple columns and ignoring the rest in output
Merge branch 'master' of https://github.com/lingpy/lingpy
Tweaking the epsilon value for gradient estimation lets Ellison (2007).
Now terminates with reasonable output on a substantial dataset.
added debug routine for msa sequences
Merge branch 'master' of https://github.com/lingpy/lingpy
update few bugs, added warning routine for orthoprofiles if profile is not detected
Much more efficient gradient estimation for Ellison (2007). Method now
feasible for hundreds of word pairs, but numerical stability issues
remain.
added error routine for non-existing orthoprofiles
Merge branch 'master' of https://github.com/lingpy/lingpy
added normalization routine to MSA class and read_msa method
updated alignment routine which now contains the new inline output of alignments as a default
Introduced a gradient check and more useful epsilon for Ellison (2007),
numerical problems remain.
Merge branch 'master' of https://github.com/lingpy/lingpy.git
update small bug failed test
Merge branch 'master' of https://github.com/lingpy/lingpy
small edits in wordlist.rc
Added equality constraint normals for Ellison (2007), numerical problems
persist.
modified json-representation, can still be parsed, but will now output in @-style
Fix import for installations without c extension.