Muscle cluster list of sequences.

    seqs: either file name or list of sequence objects or list of strings or
        single multiline string containing sequences.

    Addl docs coming soon

def cluster_seqs(seqs,
                 neighbor_join=False,
                 params={},
                 add_seq_names=True,
                 WorkingDir=tempfile.gettempdir(),
                 SuppressStderr=None,
                 SuppressStdout=None,
                 max_chars=1000000,
                 max_hours=1.0,
                 constructor=PhyloNode,
                 clean_up=True
                 ):
    """Muscle cluster list of sequences.

    seqs: either file name or list of sequence objects or list of strings or
        single multiline string containing sequences.

    Addl docs coming soon
    """
    num_seqs = len(seqs)
    if num_seqs < 2:
        raise ValueError, "Muscle requres 2 or more sequences to cluster."


    num_chars = sum(map(len, seqs))
    if num_chars > max_chars:
        params["-maxiters"] = 2
        params["-diags1"] = True
        params["-sv"] = True
        #params["-distance1"] = "kmer6_6"
        #params["-distance1"] = "kmer20_3"
        #params["-distance1"] = "kbit20_3"
        print "lots of chars, using fast align", num_chars


    params["-maxhours"] = max_hours
    #params["-maxiters"] = 10

    #cluster_type = "upgmb"
    #if neighbor_join:
    #    cluster_type = "neighborjoining"

    params["-clusteronly"] = True
    params["-tree1"] = get_tmp_filename(WorkingDir)

    muscle_res = muscle_seqs(seqs,
                 params=params,
                 add_seq_names=add_seq_names,
                 WorkingDir=WorkingDir,
                 SuppressStderr=SuppressStderr,
                 SuppressStdout=SuppressStdout)

    tree = DndParser(muscle_res["Tree1Out"], constructor=constructor)

    if clean_up:
        muscle_res.cleanUp()
    return tree