alignment.c File Reference

Collection of routines for reading alignments. More...


static pllAlignmentDatapllParsePHYLIP (const char *filename)
 Parse a PHYLIP file. More...
static pllAlignmentDatapllParseFASTA (const char *filename)
 Parse a FASTA file. More...
static int read_phylip_header (int *inp, int *sequenceCount, int *sequenceLength)
 Parse the PHYLIP file header.
static int parsedOk (int *actLen, int sequenceCount, int sequenceLength)
static int parse_phylip (pllAlignmentData *alignmentData, int input)
 Parse the PHYLIP file body.
static int getFastaAlignmentInfo (int *inp, int *seqCount, int *seqLen)
 Get information about the FASTA alignment. More...
static int parseFastaAlignment (pllAlignmentData *alignmentData, int input)
 Check whether the FASTA content is valid.
static int printTokens (int input)
pllAlignmentDatapllInitAlignmentData (int sequenceCount, int sequenceLength)
 Initialize alignment structure fields. More...
void pllAlignmentDataDestroy (pllAlignmentData *alignmentData)
 Deallocates the memory associated with the alignment data structure. More...
void pllAlignmentDataDumpConsole (pllAlignmentData *alignmentData)
 Prints the alignment to the console. More...
int pllAlignmentDataDumpFile (pllAlignmentData *alignmentData, int fileFormat, const char *filename)
 Dump the alignment to a file of format fileFormat. More...
pllAlignmentDatapllParseAlignmentFile (int fileType, const char *filename)
 Parse a file that contains a multiple sequence alignment. More...

Detailed Description

Collection of routines for reading alignments.

PLL (version 1.0.0) a software library for phylogenetic inference

Copyright (C) 2013 Tomas Flouri and Alexandros Stamatakis

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see

For any other enquiries send an Email to Tomas Flouri

When publishing work that uses PLL please cite PLL

Auxiliary functions for storing alignments read from predefined file formats