<p>I am very new to <a href="http://jorgensen.biology.utah.edu/wayned/ape/" rel="nofollow noreferrer">APE</a> software. I am trying to align complementary oligo-DNA strands using APE on macOS. I have both the forward and reverse sequence of an oligo-DNA insert in two separate files. But I am unable to align them as complementary sequences and show the sticky ends.</p>

<p>Is it possible with APE? I tried <strong>Align two sequences</strong> option. But couldn't get the expected result.</p>

CC BY-SA 4.0
2019-02-26T13:40:39.073Z
I added a link to the tool I am guessing you are using. Please correct it if it's the wrong tool. Also, please show us the result you get so we understand the problem. Does the program crash? Does it not align? Does it give a bad alignment? Does it just not give the one you were expecting?
terdon
CC BY-SA 4.0
2019-02-26T15:41:16.870Z
The link is important because of confusion with R's "ape" package. I'll check it out. Are you using Mac or PC?
M__
CC BY-SA 4.0
2019-02-26T15:42:11.560Z
@Michael G. I am using Mac
Science123
CC BY-SA 4.0
2019-02-26T16:12:14.810Z
Thanks @Vikram . Yes, me too, I'll take a look.
M__
CC BY-SA 4.0
2019-08-08T06:06:01.233Z
Could you upload the files you are trying to use as input? Or paste the text in?
Maximilian Press
CC BY-SA 4.0
2020-09-06T01:45:44.030Z
@Science123, Don't know if this is what you are looking for but here is the code for a minimal working example of using APE to produce a tree from a multiplesequencealignment loaded from a file; https://bioinformatics.stackexchange.com/a/14160/9311
Vass
<phylogenetics>
Aligning nucleotide sequences in APE software
# Aligning nucleotide sequences in APE software

(Asked by: username_0 on 2019-02-26)

I am very new to [APE](http://jorgensen.biology.utah.edu/wayned/ape/) software. I am trying to align complementary oligo-DNA strands using APE on macOS. I have both the forward and reverse sequence of an oligo-DNA insert in two separate files. But I am unable to align them as complementary sequences and show the sticky ends.

Is it possible with APE? I tried **Align two sequences** option. But couldn't get the expected result.

**Tags:** phylogenetics
> **Comments:**
> **username_1**: I added a link to the tool I am guessing you are using. Please correct it if it's the wrong tool. Also, please show us the result you get so we understand the problem. Does the program crash? Does it not align? Does it give a bad alignment? Does it just not give the one you were expecting?  
> **username_2**: The link is important because of confusion with R's "ape" package. I'll check it out. Are you using Mac or PC?  
> **username_0**: @Michael G. I am using Mac  
> **username_2**: Thanks @Vikram . Yes, me too, I'll take a look.  
> **username_3**: Could you upload the files you are trying to use as input? Or paste the text in?  
> **username_4**: @Science123, Don't know if this is what you are looking for but here is the code for a minimal working example of using APE to produce a tree from a multiplesequencealignment loaded from a file; https://bioinformatics.stackexchange.com/a/14160/9311  

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## 0 answers

