Using ESTs for phylogenomics: Can one accurately infer a phylogenetic tree from a gappy alignment?

Table 1 ANOVA with response variable stQD.

Parameters	NJ	MP	ML	SIAa	SIAb
length	***	***	***	***	***
rate	*	***	**	*
seqs	***	***	***	***	***
topol	***	***	***	**	***
gap	***	***	***	***	***
length:rate	**	**
length:seqs	***	***	***	*	***
rate:seqs		***	***
length:topol			***	***	**
rate:topol	***	***	***	***	**
seqs:topol	***	***	***	***	**
length:gap	***	***	***	***	**
rate:gap				***
seqs:gap	***	***	***	***	***
topol:gap	***	***	***	***	***
length:rate:seqs
length:rate:topol	***	*	**	**	**
length:rate:topol		***	***	***	***
rate:seqs:topol
length:rate:gap
length:seqs:gap	***	***	***	***	***
rate:seqs:gap				***
length:topol:gap	**	***	***	***	***
rate:topol:gap
seqs:topol:gap		***	***	***	***
length:rate:seqs:topol				*
length:rate:seqs:gap				*
length:rate:topol:gap
length:seqs:topol:gap		***	*	***	***
rate:seqs:topol:gap
length:rate:seqs:topol:gap

p ≤ 0.001***, p ≤ 0.01**, p ≤ 0.05*; parameters: length = alignment length; rate = evolutionary rate; seqs = number of sequences in the alignment; topol = tree topology of true tree; gap = gap pattern applied to full alignment. SIAa refers to the full SIA trees, while SIAb refers to the pruned SIA trees.

ISSN: 2730-7182