print_alignment: function to print an ordered sequences alignment in chunks of...

In geantonicelli/firstPackage: set of wrapper functions for phylogenetic analysis

Description

this is a function that takes an alignment in phylip format made by an alignment software like clustal omega and print it to the console in an ordered display of defined sequence width the function calculates the number of letters printed so far and print this number together with the name of each sequence at the end of each chunk

Usage

print_alignment(alignment, chunksize = 60)

Arguments

alignment	object of type alignment (seqinr package) with the aligned sequences to be display. A file in format phylip is generated by an alignment software from a .fasta file containing the sequences and loaded to the R environment
chunksize	integer specifying the number of sequence letters to be printed in each chunk of display

Value

this function print the sequence alignment to the console in an ordered fashion

Author(s)

gerardo esteban antonicelli

See Also

'retrieve_seqs' 'clean_alignment' 'load_alignment' 'make_tree' 'max_parsimony'

Examples

data(phylipProt)
print_alignment(phylipProt, 80)

geantonicelli/firstPackage documentation built on Aug. 24, 2020, 3:14 a.m.