make_phylogeny.py with raxml does not remap tip names

[wasade]

First reported on the QIIME forum by Misha. An example to recreate the issue is below. The specific issue is that the tip names in the resulting tree have not been replaced with the actual sequence identifiers, making the tree unusable for subsequent use.

$ cat foo.fasta
>a
AATTGGCC
>b
AATTAATT
>c
AATTGGTT
>d
ACTTGGTT
>e
AGTTGGTT
>f
ATTTGGTT
>g
TTTTGGTT
$ make_phylogeny.py -i foo.fasta -o foo.tree --tree_method raxml_v730
$ cat foo.tree
('seq_1':0.183839822882,('seq_2':5.68085188201e-07,('seq_4':0.174061925325,('seq_3':5.68085188201e-07,('seq_5':5.68085188201e-07,'seq_6':5.68085188201e-07):0.166978704908):0.163017962148):5.68085188201e-07):5.68085188201e-07,'seq_0':2.23518333752):0.0;