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OPENSEQ.org
Katherine
Genes: A B A+B
Length: 400 350 678
Sequences: 783 3475 14
Seq/Len: 1.96 9.93 0.02
MirrorTree (Pazo et al. 2001) 0.98
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 0.02 0.57 0.02
2 0.09 0.58 0.02
5 0.25 0.59 0.02
10 0.26 0.59 0.02
20 0.26 0.59 0.02
100 0.32 0.59 0.02
∞ 0.39 0.60 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 (0.02 < 0.6).
 WARNING: The input alignment may be corrupted!
  • For sequence B, there is a high ratio (0.59 > 0.4) of paralogs.
ID Seq/Len Name Options I_Prob Status
11266 0.7 Mce4A-Mce4B Δgene:(1, 1) A:(1E-40, 8) B:(1E-40, 8) msa: HHblits (2015_06) 0.00 Done - Shared
11265 0.7 Mce4A-Mce4B Δgene:(1, 2) A:(1E-40, 8) B:(1E-40, 8) msa: HHblits (2015_06) 0.00 Done - Shared
11264 0.7 Mce4A-Mce4B Δgene:(1, 5) A:(1E-40, 8) B:(1E-40, 8) msa: HHblits (2015_06) 0.00 Done - Shared
11263 0.01 Mce4A-Mce4B Δgene:(1, 20) A:(1E-40, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
11262 0 Mce4A-Mce4B Δgene:(1, 20) A:(1E-80, 8) B:(1E-80, 8) msa: HHblits (2015_06) Killed - Shared
11253 0.71 Mce4A-Mce4B Δgene:(1, 20) A:(1E-40, 8) B:(1E-40, 8) msa: HHblits (2015_06) 0.00 Done - Shared
11244 1.08 Mce4A-Mce4B-2 Δgene:(0, 2) A:(1E-02, 8) B:(1E-02, 8) msa: HHblits (2015_06) 1.00 Done - Shared
11243 1.08 Mce4A-Mce4B-2 Δgene:(0, 1) A:(1E-02, 8) B:(1E-04, 8) msa: HHblits (2015_06) 1.00 Done - Shared
11242 1.08 Mce4A-Mce4B-2 Δgene:(0, 1) A:(1E-02, 2) B:(1E-04, 2) msa: HHblits (2015_06) 1.00 Done - Shared
11241 0.7 Mce4A-Mce4B Δgene:(1, 10) A:(1E-40, 8) B:(1E-40, 8) msa: HHblits (2015_06) 0.00 Done - Shared
11233 0.7 Katherine Δgene:(0, 1) A:(1E-40, 8) B:(1E-40, 8) msa: HHblits (2015_06) 0.00 Done - Shared
11232 0 Mce4A-Mce4B Δgene:(1, 1) A:(1E-80, 8) B:(1E-80, 8) msa: HHblits (2015_06) Killed - Shared
11231 1.08 Mce4A-Mce4B-2 Δgene:(0, 1) A:(1E-02, 2) B:(1E-02, 2) msa: HHblits (2015_06) 1.00 Done - Shared
11230 0.01 Mce4A-Mce4Bx3 Δgene:(1, 1) A:(1E-02, 8) B:(1E-02, 8) msa: HHblits (2015_06) Killed - Shared
11229 0.01 Mce4A-Mce4B-2 Δgene:(1, 100) A:(1E-02, 8) B:(1E-02, 8) msa: HHblits (2015_06) Killed - Shared
11223 0.02 Katherine Δgene:(1, 20) A:(1E-04, 8) B:(1E-04, 8) msa: HHblits (2015_06) Killed - Shared
11214 0.03 Mce4A-Mce4B Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
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