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Genes: |
A |
B |
A+B |
Length: |
273 |
440 |
635 |
Sequences: |
2296 |
3220 |
2168 |
Seq/Len: |
8.41 |
7.32 |
3.41 |
MirrorTree (Pazo et al. 2001) |
0.90 |
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Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
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Jackhmmer results
Sequence A: (Date: 2015_06) 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: 2015_06) 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 Jackhmmer 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 |
3132 |
3.41 |
cIV_C_80_cIII_cytb_60_Pdenitr |
Δgene:(1, ∞) A:(1E-80, 8) B:(1E-60, 8) msa: Jackhmmer (2015_06)
|
0.29 |
Done - Shared |
3130 |
3.53 |
cIV_C_60_cIII_cytb_60_Pdenitr |
Δgene:(1, ∞) A:(1E-60, 8) B:(1E-60, 8) msa: Jackhmmer (2015_06)
|
0.33 |
Done - Shared |
3129 |
3.59 |
cIV_C_40_cIII_cytb_60_Pdenitr |
Δgene:(1, ∞) A:(1E-40, 8) B:(1E-60, 8) msa: Jackhmmer (2015_06)
|
0.12 |
Done - Shared |
3128 |
3.65 |
cIV_C_20_cIII_cytb_40_Pdenitr |
Δgene:(1, ∞) A:(1E-20, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06)
|
0.05 |
Done - Shared |
3127 |
3.6 |
cIV_C_40_cIII_cytb_20_Pdenitr |
Δgene:(1, ∞) A:(1E-40, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06)
|
0.09 |
Done - Shared |
3126 |
3.62 |
cIV_C_40_cIII_cytb_40_Pdenitr |
Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06)
|
0.10 |
Done - Shared |