Software for counting mutations over a tree

Question

[confusedious]

Hi everyone,

I have a nucleotide alignment in .fasta format and a phylogenetic tree for these data in .newick format.

I'd like to find some software that can count how many times each variable position in the alignment needs to change over a given tree tree (interpreting the mutations in the most parsimonious way).

Does anyone have any suggestions?

Answer 1

[confusedious]

I found that an estimation of the maximum mutation count at each position can be obtained using Fluxus Network's statistics tool after building a Median Joining network.

See: http://www.fluxus-engineering.com/sharenet.htm

Answer 2

[jhc]

This script might be useful:

	from collections import defaultdict
	from ete3 import PhyloTree, TreeStyle, SeqMotifFace, TextFace, RectFace
	alg = """
	>Dme_001
	MAEIPDETIQQFMALT---HNIAVQYLSEFGDLNEAL--YYASQTDDIKDRREEAH
	>Dme_002
	MAEIPDATIQQFMALTNVSHNIAVQY--EFGDLNEALNSYYAYQTDDQKDRREEAH
	>Cfa_001
	MAEIPDATIQ---ALTNVSHNIAVQYLSEFGDLNEALNSYYASQTDDQPDRREEAH
	>Mms_001
	MAEAPDETIQQFMALTNVSHNIAVQYLSEFGDLNEAL--------------REEAH
	>Hsa_001
	MAEIPDETIQQFMALT---HNIAVQYLSEFGDLNEALNSYYASQTDDIKDRREEAH
	>Ptr_002
	MAEIPDATIQ-FMALTNVSHNIAVQY--EFGDLNEALNSY--YQTDDQKDRREEAH
	>Mmu_002
	MAEIPDATIQ---ALTNVSHNIAVQYLSEFGDLNEALNSYYASQTDDQPDRREEAH
	>Hsa_002
	MAEAPDETIQQFM-LTNVSHNIAVQYLSEFGDLNEAL--------------REEAH
	>Ptr_001
	MAEIPDATIQ-FMALTNVSHNIAVQY--EFGDLNEALNSY--YQTDDQKDRREEAH
	>Mmu_001
	MAEIPDTTIQ---ALTNVSHNIAVQYLSEFGDLNEALNSYYASQTDDQPDRREEAH
	"""
	def mutation_columns(sequences):
	col2diffs = defaultdict(set)
	alg_length = len(sequences[0])
	for col in xrange(alg_length):
	for seq in sequences:
	col2diffs[col].add(seq[col])
	col2diffs[col].discard('-')
	subseqs = set()
	relevant_columns = []
	for col in xrange(alg_length):
	if len(col2diffs[col]) > 1:
	relevant_columns.append(col)
	for seq in sequences:
	subseqs.add(''.join([seq[col] for col in relevant_columns]))
	return subseqs, relevant_columns
	def get_example_tree():
	# Performs a tree reconciliation analysis
	gene_tree_nw = '((Dme_001,Dme_002),(((Cfa_001,Mms_001),((Hsa_001,Ptr_001),Mmu_001)),(Ptr_002,(Hsa_002,Mmu_002))));'
	t = PhyloTree(gene_tree_nw)
	ts = TreeStyle()
	# disable default PhyloTree Layout
	ts.layout_fn = lambda x: True
	t.link_to_alignment(alg)
	node2content = t.get_cached_content()
	for node in t.traverse():
	node.img_style["size"] = 0
	if not node.is_leaf():
	leaves = node2content[node]
	# get columns with different aa
	subseqs, relevant_columns = mutation_columns([lf.sequence for lf in leaves])
	for seq in subseqs:
	f = SeqMotifFace(seq, seq_format="seq", width=10, height=8)
	f.margin_top = 2
	f.margin_right = 6
	node.add_face(f, column=0, position="branch-bottom")
	for j, col in enumerate(relevant_columns):
	col_f = RectFace(10, 10, fgcolor=None, bgcolor=None,
	label={"text":str(col), "fonttype":"Courier", "color":"black", "fontsize":6})
	node.add_face(col_f, column=j, position="branch-top")
	col_f.margin_bottom = 2
	else:
	f = SeqMotifFace(node.sequence, seq_format="seq", width=6)
	node.add_face(f, column=0, position="aligned")
	alg_length = len(lf.sequence)
	ts.draw_aligned_faces_as_table = False
	for colnum in xrange(alg_length):
	col_f = RectFace(10, 10, fgcolor=None, bgcolor=None,
	label={"text":str(colnum), "fonttype":"Courier", "color":"black", "fontsize":6})
	ts.aligned_header.add_face(col_f, column=colnum)
	return t, ts
	if __name__ == "__main__":
	t, ts = get_example_tree()
	t.show(tree_style=ts)

view raw plot_mutations.py hosted with ❤ by GitHub

It displays what mutations occurred in each branch. Should be easy to modify to just count.

Answer 3

[Joseph Hughes]

You could use Mesquite or PAUP. I believe it is also possible to do this in R using the APE package.

[confusedious]

Thank you for the suggestions. I have tried with these packages, but have only been able to get a mutation count for the whole alignment/tree combination, not a count for individual informative sites.