Key for Scholl_NodL sequence alignments:

gi|2494018 - Escherichia coli

gi|1561556 - Bacillus halodurans

gi|586845| - Bacillus subtilis

gi|128479| - Sinorhizobium meliloti

gi|128478| - Rhizobium leguminosarum

rk11c02.y1 - Meloidogyne javanica EST

MI01045    - Meloidogyne incognita cluster

gi|1347246 - Mesorhizobium loti

gi|1588765 - Agrobacterium tumefaciens

gi|1449502 - Streptomyces coelicolor

gi|6322243 - Saccharomyces cerevisiae

gi|1514602 - Lactobacillus delbrueckii 

gi|1657538 - Escherichia coli

gi|1589595 - Clostridium acetobutylicum


Both alignments are in PHYLIP format.

The first, gb-2003-4-6-R39-s10.phy, is the alignment used to calculate the tree, 
using PHYLIP's ProtDist and Neighbor Joining, as described in the 
"Materials and Methods" section of the manuscript.

The second, gb-2003-4-6-R39-s11.phy is the alignment of the original 
sequences, before any manual adjustments were made.

The key is a "translation" of the gi number listed in the alignment to the 
species as noted in the phylogeny in figure 2.

Please note that in PHYLIP's ProtDist program, gaps are treated as unknown 
and affect only pariwise distance calculations for the sequence containing 
the gap.