Minor changes

Signed-off-by: Inti Pedroso <intipedroso@gmail.com>
Merge branch 'feature/get_number_of_seq_by_taxon' of github.com:inti/Compara-Phylostratigraphy into feature/get_number_of_seq_by_taxon
Merge branch 'release/v.9.0'

This is a major release
- It implements a more robust method to obtain hard-scores
- it parse properly PARALIGN table output
- it provides functionality to calculat bootstrap confidence intervals for the phylostratum scores
- it provides several new continous scores
- several minor big were fixed
- code has been checked, tidy up, documentation improved with examples.

Inti Pedroso <intipedroso@gmail.com>
- Empty python script created
- ipython notebook with some code snippets to start the analysis.
Initial version of python module with utility functions
Initial version of main script
improved ipython notebooks. Editing and tidy up needed

Signed-off-by: Inti Pedroso <intipedroso@gmail.com>
Major changes
- code has been re-ordered.
	* functions has been coded explicitly and moved to the package file
	* Main script contains discrete commands as user would use it on the future.

Signed-off-by: Inti Pedroso <intipedroso@gmail.com>
New routines to help improve the code

Signed-off-by: Inti Pedroso <intipedroso@gmail.com>
Major changes.

Signed-off-by: Inti Pedroso <intipedroso@gmail.com>
bugs fixed
Merge branch 'feature/test_python_dev' of github.com:inti/Comparative-Phylostratigraphy into feature/get_number_of_seq_by_taxon
file added

Signed-off-by: Inti Pedroso <intipedroso@gmail.com>
Merge branch 'feature/test_python_dev' of github.com:inti/Comparative-Phylostratigraphy into feature/get_number_of_seq_by_taxon
reference added

Signed-off-by: Inti Pedroso <intipedroso@gmail.com>
minor changes
New module with function to read NCBI Taxonomy files and identify a lineage and LCAs

Signed-off-by: Inti Pedroso <intipedroso@gmail.com>
Major changes
- Improved speed and robustness of matching taxids with GIs
- a few routines added to improve code

Signed-off-by: Inti Pedroso <intipedroso@gmail.com>
Files for Perl implementation removed

Signed-off-by: Inti Pedroso <intipedroso@gmail.com>
Major changes