Initial commit for trimAl v1.4.
Now it is possible to change minimal columns block size for all methods
Make minor improvements.
Added new function to detect and remove columns/sequences composed only by gaps.
Added new function to dump selected information. Remove several instances of same code.
Finish implementation of new functions for removing columns/sequences composed only by gaps.
Refactored other functions. New simple functions have been added for reducing codex complexity and improving general code maintainability.
Exploring new implementations for making code shorther and more legible
Modified printing function for "colnumbering" option. Now it is included #ColumnsMap tag follow by a <tab> and then the correspondence between columns in the input and trimmed alignments
Remember, columns and sequences start by 0 in trimAl.
Improved report about sequences identity
Clean-up the code. Added new function to compute a less precise but faster identity matrix.
Added new program to the project. This program will be focused only on getting different stats about input alignment/s
It's a fork from trimAl main program that will have specific function.
Rewritten new program 'statAl' as a proof of concept about future code refactoring for trimAl code.
Now, "*" are accepted as part of the input sequence.
Added new functions to compute identity columns and then max, min, average and standard desv. based on these values.
Fixed minor bug for selecting lowest threshold when there are not no-gaps columns in the input alignment.
Removed extra blank line into output FASTA format files.
Added new parameter to keep sequences even when they are composed only by gaps.
Improved way to detect nature of input sequences: DNA, RNA or AminoAcids
Added new feature "-keepheader" in order to dump original sequence headers from input FASTA format files.
Extended detection of biological datatypes. Now trimAl can detect ambiguous DNA/RNA nucleotide residues such as 'B', 'W', etc.
For more information about ambiguous letter, check out http://www.ncbi.nlm.nih.gov/staff/tao/tools/tool_lettercode.html
Added new functionality to 'readAl' in order to get some useful information about input alignment (e.g. alignment length, sequence number, max or min sequence length/names, etc)
Recoded (and possibly improved) the way 'readAl' provides information (-info, -type, -format parameters) about input alignment. Now it should be easier to parse output information.
Added new file containing all #define statement on the program. On this way, it should be easier to mantain source code for trimAl, readAl & statAl.
Improve backtranslation functionality.
Now, it considers the presence of:
 .- Selenocysteines ('U') coded by the stop-codon 'TGA'.
 .- Pyrrolysines ('O') coded by the stop-codon 'TAG'.
 .- Presence of wildcards/indetermination characters such as 'B' or 'X' at amino-acidic sequence level.
Added new parameter -ignorestopcodon. It will skip controlling for stop codons in the input sequences files for the backtranslation functionality.
Updated current BUILD & building DATE for all programs
Control of Stop Codons in input CDS sequences have been sligthly relaxed.
Corrected a minor bug to read the complete collection of CDS when backtranslating - and not just up to the number of protein sequeces.