+ public Msa infer( final List<MolecularSequence> seqs, final List<String> opts ) throws IOException,
+ InterruptedException {
+ final File file = File.createTempFile( "__mafft_input_", ".fasta" );
+ file.deleteOnExit();
+ final BufferedWriter writer = new BufferedWriter( new FileWriter( file ) );
+ SequenceWriter.writeSeqs( seqs, writer, SEQ_FORMAT.FASTA, 100 );
+ writer.close();
+ final Msa msa = infer( file, opts );
+ file.delete();
+ return msa;
+ }
+
+ @Override