net.maizegenetics.dna.snp

Class ReadSequenceAlignmentUtils

net.maizegenetics.dna.snp.ReadSequenceAlignmentUtils

public class ReadSequenceAlignmentUtils

reads aligned sequence data from plain text files.

recognizes PHYLIP 3.4 INTERLEAVED, PHYLIP SEQUENTIAL, CLUSTAL and derived formats.

Other features: - the dot as "copy character" is recognized, - all base characters are capitalized, - automatic data type estimation - determination of corresponding base frequencies.

Method Detail

readBasicAlignments

public static GenotypeTable readBasicAlignments(java.io.PushbackReader input,
                                                int maxLabelLength)

read from stream, while letting the user set the maximum label (taxa) label length as non-standard phylip formats now exist

readBasicAlignments

public static GenotypeTable readBasicAlignments(java.lang.String file,
                                                int maxLabelLength)

read from file, while letting the user set the maximum label (taxa) label length as non-standard phylip formats now exist