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OPENSEQ.org
4HEA_M - 4HEA_N
Genes: A B A+B
Length: 469 427 736
Sequences: 9176 9436 19
Seq/Len: 19.57 22.1 0.03
MirrorTree (Pazo et al. 2001) 0.85
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show HHblits results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.45 0.48 0.01
2 0.48 0.50 0.01
5 0.53 0.55 0.02
10 0.55 0.57 0.02
20 0.56 0.58 0.02
100 0.61 0.62 0.02
∞ 0.75 0.77 0.02
Paired alignment generation
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
Sequence A E-value:
Iterations:
Sequence B E-value:
Iterations:
Δgene MSA
Figure 1: The effect of Δgene on ratio of paralogs in the genome for each gene, and the number of sequences in the resulting joined alignment. Figure 2: Distribution of Δgene across all genomes. Figure 3: Current parameters. You can use the form to adjust the parameters and resubmit the job!
GREMLIN results
  • ERROR: Not enough sequences to run GREMLIN analysis on (0.03 < 0.6).
 WARNING: The input alignment may be corrupted!
  • For sequence A, there is a high ratio (0.56 > 0.4) of paralogs.
  • For sequence B, there is a high ratio (0.58 > 0.4) of paralogs.
ID Seq/Len Name Options I_Prob Status
0004 1.09 M N Δgene:(1, 20) A:(1E-80, 8) B:(1E-80, 8) (2013_03) 0.91 Done - Shared
0003 0.03 M N Δgene:(1, 20) A:(1E-60, 8) B:(1E-60, 8) (2013_03) Killed - Shared
0002 0.03 4HEA_M - 4HEA_N Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) (2013_03) Killed - Shared
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