A handful of tools developed to facilitate any workflow in bioinformatics. Specially useful for research in phylogenomics (often stalled by overwhelming amounts of DNA and big trees).
From a multigb file (obtained with any quick search of interest in GenBank), this script captures only the coding section (CDS) for each sequence and outputs them into a simpified fasta (multisequence file format) for each gene found. These fasta files keep info like species name and accession number for each sequence in the database. Aditionally, the script automatically filters CDSs by their size, so that each fasta includes only the longest CDS for each species it represents, maximizing data utilization for phylogenetics.
call: perl multiGB2fasta.pl <multigbfile.gb>
Provided a multisequence file in fasta format and a txt file containing a list of patterns (such as species names and/or accession numbers), this script produces a new fasta file containing only those sequences that match at least one of the patterns passed.
call: perl seqSelector.pl <sequencefile.fasta> <patternlist.txt>
Here '-vv' stands for vice-versa. This script simply converts any sequence alignment in fasta or sequential phylip format to the other one. Specific format extensions (like .fasta or .phy) must not be a concern, since fasta2phylip-vv identifies the file format by its content (the same is true to all other scripts in BItools);
call: perl fasta2phylip-vv.pl <alignmentfile.[fasta|phy]>
Provided a sequence alignment file in sequential phylip format, outputs a new version of the file free of gap-only sites (which are void of useful information for phylogenetic analyses).
call: perl noGapOnlySites.pl <alignmentfile.phy>
Trims the gappy edges of the given sequence alignment (fasta format). Provided a numeric threshold (%), it eliminates all sites on both flanking regions of the alignment up to any with gap-percentage below this threshold. The output is a sequential fasta file with all remaining sites.
call: perl trimmer.pl <alignmentfile.fasta> <flanking-gap-threshold(%)>
Like trimmer.pl but also eliminates all middle sites which absolute number of gaps surpasses another given numeric threshold.
call: perl zblocks.pl <alignmentfile.fasta> <flanking-gap-threshold(%)> <middle-gap-threshold(# )>
Concatenates all fasta sequence alignments in working directory that present one specified extension. Optionaly, outputs a separate file discriminating positions of all original aligments into the concatenated one (i.e. a partitions file).
call perl concatenator.pl
Returns the total gap proportion of the given sequence alignment (fasta or sequential phylip format).
call: perl gapcounter.pl <alignmentfile.[fasta|phy]>
Provided a DNA sequence alignment (fasta or sequential phylip format), returns a tab separated table including its length (i.e. number of sites) and total proportions of gap and each nucleotide base type in the alignment (A, T, G, C and also pyrimidines [C|T|Y], purines [G|A|R], strong bases [C|G], weak bases [A|T] and undetermined bases [N|X|?]).
call: perl basereader.pl <alignmentfile.[fasta|phy]
Same as basereader.pl but also discriminates partial base proportions for each type of codon position (first, second and third) across the alignment. This feature demands the input sequence aligment to contain CDS only.
call: perl basereader.pl <alignmentfile.[fasta|phy]
Like basereader.pl but returns in-site proportions for all sites across the sequence alignment. Each row on the table now represents a specific site, from the first one to the last.
call: perl basereader.pl <alignmentfile.[fasta|phy]
C functions for codon-to-aminoacid convertions.
Add the line #include "codontools.h" to the headers of your main source code and make sure to place codontools.c, codontools.h, utilslib.c and utilslib.h files in the directory where you intend to compile the source code. Then, include codontools.c and utilslib.c when compiling (e.g. gcc -o my_exec my_main.c codontools.c utilslib.c).
prototype: char* RNAtoAA(char *codon);
Translates input RNA codon string to corresponding aminoacid string.
prototype: char** AAtoRNA(char *amino, int *ncodons);
Does the reverse of RNAtoAA(). Provided a pointer to a capitalized, underline separated (if composite) aminoacid name (e.g. 'Glutamic_acid'), it returns the pointer to an array of strings containing all RNA codons that such AA could have been translated from. It also assigns the length of this array of codons to a user-given int pointer.
prototype: char** synonyms(char *codon, int *ncodons);
Returns the array of codons that are synonymous to a user-provided one. It assigns the length of such array to a given int pointer as well.
Given an input file containing a newick format (i.e. parenthetic) tree, returns its total length (sum of all branch lengths).
call: perl treelength.pl <treefile.nwk>
R function that takes as input a phylo format tree and the IDs to any two nodes of the tree (internal and/or edge nodes - ID can be a taxon name in the latter case), returning the shortest path distance between them. This distance will correspond to the total number of branches in the path (by default) or to the sum of their lengths (if length.sensitive=TRUE is specified as well).
Perl subroutine to unroot any newick tree given as argument.
Perl subroutine that returns the partition difference between two unrooted newick trees given as arguments. By defaulf, the partition difference here is the absolute number of partitions not shared by these trees (a.k.a. Penny-Hendy or Robinson-Foulds distance) or the same number weighted by the branch lengths that represent each partition if option 1 is specified as a third argument (Kuhner-Felsenstein or 'branch score' distance). In the latter case, differences in branch lengths of partitions that are shared are also considered.