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OPENSEQ.org
NR
Genes: A B A+B
Length: 155 108 261
Sequences: 279 106 96
Seq/Len: 1.8 0.98 0.37
MirrorTree (Pazo et al. 2001) 0.91
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 0.00 0.37
2 0.00 0.00 0.37
5 0.00 0.00 0.37
10 0.00 0.00 0.37
20 0.00 0.00 0.37
100 0.00 0.00 0.37
∞ 0.02 0.00 0.37
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 (0.37 < 0.6).
ID Seq/Len Name Options I_Prob Status
1131 0 N and R Δgene:(0, 5) A:(1E-60, 8) B:(1E-60, 8) msa: HHblits (2013_03) Killed
1120 0 N and R Δgene:(0, 2) A:(1E-80, 8) B:(1E-80, 8) msa: HHblits (2013_03) Killed
1119 0.88 NR Δgene:(0, 5) A:(1E-06, 8) B:(1E-06, 8) msa: HHblits (2013_03) 0.01 Done - Shared
1118 0.52 NR Δgene:(0, 5) A:(1E-10, 8) B:(1E-10, 8) msa: Jackhmmer (2014_03) 0.29 Done
1117 0.88 NR Δgene:(0, 2) A:(1E-06, 8) B:(1E-06, 8) msa: HHblits (2013_03) 0.01 Done - Shared
1116 0.75 NR Δgene:(0, 2) A:(1E-10, 8) B:(1E-10, 8) msa: HHblits (2013_03) 0.10 Done - Shared
1115 0.75 NR Δgene:(0, 5) A:(1E-10, 8) B:(1E-10, 8) msa: HHblits (2013_03) 0.27 Done - Shared
1114 0.37 NR Δgene:(0, 2) A:(1E-10, 8) B:(1E-20, 8) msa: HHblits (2013_03) Killed - Shared
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