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OPENSEQ.org
3RPF_AC
Genes: A B A+B
Length: 143 74 216
Sequences: 41 40 43
Seq/Len: 0.29 0.54 0.2
MirrorTree (Pazo et al. 2001) 0.47
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 0.00 1.00 0.20
2 0.00 1.00 0.20
5 0.00 1.00 0.20
10 0.00 1.00 0.20
20 0.00 1.00 0.20
100 0.00 1.00 0.20
∞ 0.00 1.00 0.20
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 (0.2 < 0.6).
 WARNING: The input alignment may be corrupted!
  • For sequence B, there is a high ratio (1.00 > 0.4) of paralogs.
ID Seq/Len Name Options I_Prob Status
13630 0.31 3RPF_C Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
0140 4.71 3RPF_AC Δgene:(1, 20) A:(1E-06, 8) B:(1E-06, 8) msa: Jackhmmer (2014_03) 1.00 Done - Shared
0138 0.21 3RPF_AC Δgene:(1, 20) A:(1E-10, 8) B:(1E-10, 8) msa: Jackhmmer (2014_03) Killed - Shared
0135 0.2 3RPF_AC Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2014_03) Killed - Shared
0134 4.07 3RPF_AC Δgene:(1, 20) A:(1E-10, 8) B:(1E-10, 8) msa: HHblits (2013_03) 0.99 Done - Shared
0133 0.2 3RPF_AC Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2013_03) Killed - Shared
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