PyPHLAWD clusters
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Chloe Drummond
May 17, 2018, 12:56:18 PM5/17/18
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Hi,
I am running PyPHLAWD to get gene/intron alignments for a family. I have taken a different approach in the past, using R to search NCBI for specific gene/intron regions, but I thought I would try out this program, which relies on clustering.
I noticed that the info.html file prints a description of what's in each cluster (I'm assuming it prints the text from the description of the first accession in the cluster). However, I also noticed that some regions (ITS, for example) are repeated among clusters. What is causing this to happen, and if I try to run PyPHLAWD to generate a tree, will it count these clusters as two separate loci?
I am also running it with the tree function turned on, but the trees files are empty at the end of each run. I am trouble shooting this now, but I wonder if there is some probable mistake I might be making?
Thank you for your help!
-Chloe
Stephen Smith
May 17, 2018, 1:02:28 PM5/17/18
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Hi Chloe
Would you mind sharing what analysis you are running so I can quickly
replicate and let you know what is happening?
Take care
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Would you mind sharing what analysis you are running so I can quickly
replicate and let you know what is happening?
Take care
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Chloe Drummond
May 17, 2018, 1:20:15 PM5/17/18
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Hi Stephen,
I'm attaching the conf.py file. I kept it all pretty much at default, since I was just trying it out.
The line of code I wrote was:
> python setup_clade.py Rubus ../PHLAWD/pln.db ../Rubus_pyphlawd/
And I did this for Rosaceae as well.
Thank you for looking into it!
-Chloe
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Chloe Pak Drummond
PhD Candidate
Department of Botany
University of Wisconsin-Madison
430 Lincoln Drive
Madison, WI 53706
Tel: (917) 685-0141
E-mail: cdru...@wisc.edu
Stephen Smith
May 17, 2018, 1:45:51 PM5/17/18
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Hi Chloe
This is what I get. Does that look right?
On Thu, May 17, 2018 at 1:19 PM, Chloe Drummond
>> > email to phlawd+un...@googlegroups.com.
This is what I get. Does that look right?
On Thu, May 17, 2018 at 1:19 PM, Chloe Drummond
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> 430 Lincoln Drive
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> Chloe Pak Drummond
> PhD Candidate
> Department of Botany
> University of Wisconsin-Madison
> 430 Lincoln Drive
> Madison, WI 53706
>
> Tel: (917) 685-0141
> E-mail: cdru...@wisc.edu
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Chloe Drummond
May 17, 2018, 2:01:04 PM5/17/18
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Hi Stephen,
Yes, those are the same clusters that I got back.
-Chloe
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> Department of Botany
> University of Wisconsin-Madison
> 430 Lincoln Drive
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> E-mail: cdru...@wisc.edu
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Stephen Smith
May 17, 2018, 2:03:15 PM5/17/18
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OK, so it is that the aligned lengths don't overlap enough. The ones
that are splitting aren't getting matched together (probably will
product unreliable merged alignemnts). Does that make sense?
Not sure if you would want them back together
On Thu, May 17, 2018 at 2:00 PM, Chloe Drummond
>> >> > email to phlawd+un...@googlegroups.com.
that are splitting aren't getting matched together (probably will
product unreliable merged alignemnts). Does that make sense?
Not sure if you would want them back together
On Thu, May 17, 2018 at 2:00 PM, Chloe Drummond
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>> > Department of Botany
>> > University of Wisconsin-Madison
>> > 430 Lincoln Drive
>> > Madison, WI 53706
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>> > Department of Botany
>> > University of Wisconsin-Madison
>> > 430 Lincoln Drive
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> Department of Botany
> University of Wisconsin-Madison
> 430 Lincoln Drive
> Madison, WI 53706
>
> Tel: (917) 685-0141
> E-mail: cdru...@wisc.edu
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> Chloe Pak Drummond
> PhD Candidate
> Department of Botany
> University of Wisconsin-Madison
> 430 Lincoln Drive
> Madison, WI 53706
>
> Tel: (917) 685-0141
> E-mail: cdru...@wisc.edu
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Chloe Drummond
May 17, 2018, 2:09:53 PM5/17/18
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That makes sense. It is nice that these get filtered out, so to speak, since grabbing sequences by name would not do this. I will extract the .fa files for the clusters that by description should go together, and take a closer look.
I am also wondering whether the clustering does reverse complementing? There was one taxon (Rubus palmatus) from this dataset that needed to be reverse complemented in cluster 2 (matK), but I did not see any other issue like this in the other clusters.
Thank you again for your help,
Chloe
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>> > Department of Botany
>> > University of Wisconsin-Madison
>> > 430 Lincoln Drive
>> > Madison, WI 53706
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>> > Tel: (917) 685-0141
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> Chloe Pak Drummond
> PhD Candidate
> Department of Botany
> University of Wisconsin-Madison
> 430 Lincoln Drive
> Madison, WI 53706
>
> Tel: (917) 685-0141
> E-mail: cdru...@wisc.edu
>
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Stephen Smith
May 17, 2018, 2:14:31 PM5/17/18
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Reverse complements should definitely be taken care of in the aligned
file. This is done in an automated fashion though so it is possible
(though unlikely) that there could be one that is missed.
If you note an error there though, please share and I can try and
track it down real quick
Thanks!
On Thu, May 17, 2018 at 2:09 PM, Chloe Drummond
>> >> >> > email to phlawd+un...@googlegroups.com.
file. This is done in an automated fashion though so it is possible
(though unlikely) that there could be one that is missed.
If you note an error there though, please share and I can try and
track it down real quick
Thanks!
On Thu, May 17, 2018 at 2:09 PM, Chloe Drummond
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>> >> > --
>> >> > Chloe Pak Drummond
>> >> > PhD Candidate
>> >> > Department of Botany
>> >> > University of Wisconsin-Madison
>> >> > 430 Lincoln Drive
>> >> > Madison, WI 53706
>> >> >
>> >> > Tel: (917) 685-0141
>> >> > E-mail: cdru...@wisc.edu
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>> >> > Chloe Pak Drummond
>> >> > PhD Candidate
>> >> > Department of Botany
>> >> > University of Wisconsin-Madison
>> >> > 430 Lincoln Drive
>> >> > Madison, WI 53706
>> >> >
>> >> > Tel: (917) 685-0141
>> >> > E-mail: cdru...@wisc.edu
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>> > PhD Candidate
>> > Department of Botany
>> > University of Wisconsin-Madison
>> > 430 Lincoln Drive
>> > Madison, WI 53706
>> >
>> > Tel: (917) 685-0141
>> > E-mail: cdru...@wisc.edu
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>> > PhD Candidate
>> > Department of Botany
>> > University of Wisconsin-Madison
>> > 430 Lincoln Drive
>> > Madison, WI 53706
>> >
>> > Tel: (917) 685-0141
>> > E-mail: cdru...@wisc.edu
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> Chloe Pak Drummond
> PhD Candidate
> Department of Botany
> University of Wisconsin-Madison
> 430 Lincoln Drive
> Madison, WI 53706
>
> Tel: (917) 685-0141
> E-mail: cdru...@wisc.edu
>
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> Chloe Pak Drummond
> PhD Candidate
> Department of Botany
> University of Wisconsin-Madison
> 430 Lincoln Drive
> Madison, WI 53706
>
> Tel: (917) 685-0141
> E-mail: cdru...@wisc.edu
>
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Chloe Drummond
May 17, 2018, 4:53:50 PM5/17/18
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Ah, I think I figured out the issue. I used the individual .fa files to make my own alignments, since I couldn't figure out how to manipulate the .aln file type!
If I had used the pyphlawd .aln files, I'm sure the reverse complementing would have been taken care of. Sorry for the confusion.
-Chloe
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>> >> > --
>> >> > Chloe Pak Drummond
>> >> > PhD Candidate
>> >> > Department of Botany
>> >> > University of Wisconsin-Madison
>> >> > 430 Lincoln Drive
>> >> > Madison, WI 53706
>> >> >
>> >> > Tel: (917) 685-0141
>> >> > E-mail: cdru...@wisc.edu
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>> >
>> >
>> >
>> > --
>> > Chloe Pak Drummond
>> > PhD Candidate
>> > Department of Botany
>> > University of Wisconsin-Madison
>> > 430 Lincoln Drive
>> > Madison, WI 53706
>> >
>> > Tel: (917) 685-0141
>> > E-mail: cdru...@wisc.edu
>> >
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> Chloe Pak Drummond
> PhD Candidate
> Department of Botany
> University of Wisconsin-Madison
> 430 Lincoln Drive
> Madison, WI 53706
>
> Tel: (917) 685-0141
> E-mail: cdru...@wisc.edu
>
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Stephen Smith
May 17, 2018, 4:57:24 PM5/17/18
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great!
On Thu, May 17, 2018 at 4:53 PM, Chloe Drummond
>> >> >> >> > email to phlawd+un...@googlegroups.com.
On Thu, May 17, 2018 at 4:53 PM, Chloe Drummond
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>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> > --
>> >> >> > Chloe Pak Drummond
>> >> >> > PhD Candidate
>> >> >> > Department of Botany
>> >> >> > University of Wisconsin-Madison
>> >> >> > 430 Lincoln Drive
>> >> >> > Madison, WI 53706
>> >> >> >
>> >> >> > Tel: (917) 685-0141
>> >> >> > E-mail: cdru...@wisc.edu
>> >> >> >
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>> >> >> > Chloe Pak Drummond
>> >> >> > PhD Candidate
>> >> >> > Department of Botany
>> >> >> > University of Wisconsin-Madison
>> >> >> > 430 Lincoln Drive
>> >> >> > Madison, WI 53706
>> >> >> >
>> >> >> > Tel: (917) 685-0141
>> >> >> > E-mail: cdru...@wisc.edu
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>> >> > Chloe Pak Drummond
>> >> > PhD Candidate
>> >> > Department of Botany
>> >> > University of Wisconsin-Madison
>> >> > 430 Lincoln Drive
>> >> > Madison, WI 53706
>> >> >
>> >> > Tel: (917) 685-0141
>> >> > E-mail: cdru...@wisc.edu
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>> >> > Chloe Pak Drummond
>> >> > PhD Candidate
>> >> > Department of Botany
>> >> > University of Wisconsin-Madison
>> >> > 430 Lincoln Drive
>> >> > Madison, WI 53706
>> >> >
>> >> > Tel: (917) 685-0141
>> >> > E-mail: cdru...@wisc.edu
>> >> >
>> >> > --
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>> >
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>> >
>> >
>> > --
>> > Chloe Pak Drummond
>> > PhD Candidate
>> > Department of Botany
>> > University of Wisconsin-Madison
>> > 430 Lincoln Drive
>> > Madison, WI 53706
>> >
>> > Tel: (917) 685-0141
>> > E-mail: cdru...@wisc.edu
>> >
>> > --
>> > You received this message because you are subscribed to the Google
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>> > "phlawd" group.
>> > To unsubscribe from this group and stop receiving emails from it, send
>> > an
>> > email to phlawd+un...@googlegroups.com.
>> >
>> >
>> >
>> >
>> > --
>> > Chloe Pak Drummond
>> > PhD Candidate
>> > Department of Botany
>> > University of Wisconsin-Madison
>> > 430 Lincoln Drive
>> > Madison, WI 53706
>> >
>> > Tel: (917) 685-0141
>> > E-mail: cdru...@wisc.edu
>> >
>> > --
>> > You received this message because you are subscribed to the Google
>> > Groups
>> > "phlawd" group.
>> > To unsubscribe from this group and stop receiving emails from it, send
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>>
>> --
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>>
>> --
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>> For more options, visit https://groups.google.com/d/optout.
>
>
>
>
> --
> Chloe Pak Drummond
> PhD Candidate
> Department of Botany
> University of Wisconsin-Madison
> 430 Lincoln Drive
> Madison, WI 53706
>
> Tel: (917) 685-0141
> E-mail: cdru...@wisc.edu
>
> --
> You received this message because you are subscribed to the Google Groups
> "phlawd" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to phlawd+un...@googlegroups.com.
>
>
>
>
> --
> Chloe Pak Drummond
> PhD Candidate
> Department of Botany
> University of Wisconsin-Madison
> 430 Lincoln Drive
> Madison, WI 53706
>
> Tel: (917) 685-0141
> E-mail: cdru...@wisc.edu
>
> --
> You received this message because you are subscribed to the Google Groups
> "phlawd" group.
> To unsubscribe from this group and stop receiving emails from it, send an
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