def read_alignments(self, input_dir, file_format, header_grep=None):
        """ Get list of alignment files from an input directory *.fa, *.fas and
        *.phy files only

        Stores in self.files """

        compression = ['', 'gz', 'bz2']

        if file_format == 'fasta':
            extensions = ['fa', 'fas', 'fasta']

        elif file_format == 'phylip':
            extensions = ['phy']

        else:
            extensions = []

        extensions = list('.'.join([x,y]) if y else x for x,y in itertools.product(extensions, compression))

        files = fileIO.glob_by_extensions(input_dir, extensions)
        files.sort(key=SORT_KEY)
        self._input_files = files
        records = []

        if self.show_progress:
            pbar = setup_progressbar("Loading files", len(files), simple_progress=True)
            pbar.start()

        for i, f in enumerate(files):
            if f.endswith('.gz') or f.endswith('.bz2'):
                fd, tmpfile = tempfile.mkstemp()
                with fileIO.freader(f, f.endswith('.gz'), f.endswith('.bz2')) as reader,\
                     fileIO.fwriter(tmpfile) as writer:
                    for line in reader:
                        if ISPY3:
                            line = line.decode()
                        writer.write(line)
                try:
                    record = Alignment(tmpfile, file_format, True)
                except ValueError:
                    record = Alignment(tmpfile, file_format, False)
                finally:
                    os.close(fd)
                    os.unlink(tmpfile)

            else:
                try:
                    record = Alignment(f, file_format, True)
                except RuntimeError:
                    record = Alignment(f, file_format, False)

            if header_grep:
                try:
                    datatype = 'dna' if record.is_dna() else 'protein'

                    record = Alignment([(header_grep(x), y) for (x, y) in record.get_sequences()], datatype)

                except TypeError:
                    raise TypeError("Couldn't apply header_grep to header\n"
                                    "alignment number={}, name={}\n"
                                    "header_grep={}".format(i, fileIO.strip_extensions(f), header_grep))
                except RuntimeError:
                    print('RuntimeError occurred processing alignment number={}, name={}'
                          .format(i, fileIO.strip_extensions(f)))
                    raise

            record.name = (fileIO.strip_extensions(f))
            records.append(record)
            if self.show_progress:
                pbar.update(i)
        if self.show_progress:
            pbar.finish()
        return records
Get list of alignment files from an input directory *.fa, *.fas and
        *.phy files only

        Stores in self.files