Explanation of
alignment files
The alignment files are in interleaved PHYLIP format, and can be viewed in a text editor, word processor, or various sequence analysis packages (e.g. BioEdit) that accommodate PHYLIP format.
IAAAtOnly.phy –
an alignment of the translated sequences
from the 28 Aux/IAA sequences from Arabidopsis
thaliana, obtained from GenBank.
IAAAtOnlyConsRegions.phy – the same alignment as the previous file, but regions that are not well conserved in individual Aux/IAA subgroups have been trimmed. The tree in Figure 1 of the Remington et al. manuscript was derived from this alignment.
IAAAllSpecies.phy
– a comprehensive alignment of the
translated A. thaliana Aux/IAA
sequences, plus sequences
obtained from Medicago truncatula, Oryza sativa
(rice), Pinus pinaster, and Physcomitrella patens.
Alignments between the A. thaliana
sequences are different in some cases from those in the two previous
files. Some apparent errors in sequences
from
expressed sequence tags (ESTs) have been
corrected to
obtain more probable reading frames.
IAAAllSpeciesConsRegions.phy – the same alignment as the previous file, but regions that are not well conserved in individual Aux/IAA subgroups have been trimmed. This is one of the three alignments from which the consensus tree in Figure 6 was constructed.
IAAAtOnlyConsRegionsAlt.phy
– an alternate alignment of
conserved regions of the A. thaliana Aux/IAA
loci, identical to the above
alignment but consisting of only the A.
thaliana sequences.
ARFAt.phy – an
alignment of the translated sequences from
the 23 A. thaliana ARF loci, plus a
mtDNA fragment showing strong ARF
similarity. Some
annotations have been modified by Tom Guilfoyle
from
those in GenBank.
ARFAtConsRegions.phy
– the same alignment as the previous file,
but containing only the conserved regions.
The tree in Figure 5 was derived from this alignment.
ARFAtOs.phy – a
comprehensive alignment of translated A. thaliana
sequences with ARF sequences from Oryza sativa.
ARFAtOsConsRegions.phy
– the same alignment as the previous
file, but containing only the conserved regions. Branching
positions of rice ARF sequences indicated in Figure 5
was
derived from a neighbor-joining tree constructed from this alignment.
IAAPlusARFAtConsRegions.phy – an alignment of translated sequences of conserved regions of the A. thaliana Aux/IAA loci with the motifs III-IV of 7 ARF loci selected to represent the main ARF groups. Phylogenetic trees constructed from this alignment were used to establish the root positions of the Aux/IAA and ARF trees used in the Remington et al. manuscript.