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Genes: |
A |
B |
A+B |
Length: |
155 |
108 |
255 |
Sequences: |
284 |
345 |
224 |
Seq/Len: |
1.83 |
3.19 |
0.88 |
MirrorTree (Pazo et al. 2001) |
0.87 |
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Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
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HHblits results
Sequence A: (Date: 2013_03) BEFORE and AFTER the coverage filter was applied, to remove sequences that don't cover at least 75% of query length. Regions above red line, indicates positions where there is > 5 sequences per length (if visible, green bar = 20 seq/len). Point of this graphic is to give you an idea if resubmitting a sub-portion of your sequence might help increase the overall Seq/Len.
Sequence B: (Date: 2013_03) BEFORE and AFTER the coverage filter was applied, to remove sequences that don't cover at least 75% of query length. Regions above red line, indicates positions where there is > 5 sequences per length (if visible, green bar = 20 seq/len). Point of this graphic is to give you an idea if resubmitting a sub-portion of your sequence might help increase the overall Seq/Len.
[Show HHblits results] - Maybe useful in deciding what regions to trim. |
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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! |
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)
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Killed |
1120 |
0 |
N and R |
Δgene:(0, 2) A:(1E-80, 8) B:(1E-80, 8) msa: HHblits (2013_03)
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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)
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Killed - Shared |