I have my sequences alignment in fasta file and mega file but i can not upload the file on PopArt software since it needs the file in nexus format. Can you please help in converting the fasta /mega file into nexus format or recommending which software i am supposed to use.
There are online services for that, such as:
http://sequenceconversion.bugaco.com/converter/biology/sequences/fasta_to_nexus.php
best regards,
---sram
You can use MEGA, open your FASTA sequence and export to NEXUS file.
try out below python code i wrote for fasta to nexus conversion
#fasta to nexus conversion
f = open("sample.fa", "r")
lines=f.readlines()
nc=len(lines[1])
f1 = open('outputsample.nex', 'a')
f1.write("#NEXUS")
f1.write("\n")
f1.write("begin data;")
f1.write("\n")
f1.write("Dimensions ntax="+file_len("sample.fa")+"\t"+"nchar="+nc+";")
f1.write("\n")
f1.write("Format datatype=dna missing=? gap=-;")
f1.write("\n")
f1.write("Matrix")
f1.write("\n")
i=0
j=1
for l in lines:
f1.write(lines[i]+"\t"+"lines[j]")
f1.write("\n")
if j>file_len("sample.fa"):
break
i=i+2
j=j+2
f1.write("\n")
f1.write(";")
def file_len(fname):
with open(fname) as f:
for i, l in enumerate(f):
pass
return i + 1
Hi Thandy
I ran into the same question this morning. I just couldn't get the fasta file to turn into the nexus file for Mrbayes to open properly. I just talked to my professor Dr. Jeffery Mower and he taught me how to use mega to change the file. So actually the credit for this piece of knowledge should go to Dr. Mower in UNL. I want to share it when the memory is still fresh.
1. If your fasta taxa names contain space " ". Go to the file and use "edit" "replace" and replace all the spaces into underline "_". Nexus does not like space.
2. If your file is "txt" Mega won't recognize it. Go to your file "save as" and change the whatever it is to .fas, and also change the file type to "all files"
3. Then open mega, file, open file, choose "analysis". Then mega should open the aligned file fine.
4. Export the file in Nexus format. For my dataset he suggested don't choose the option of "interleaved output" but I am not sure it is the best option for everyone.
Then try to open it with Mrbayes or other software you are planning on using the nexus file to test if it works!
I know this is too late for you who asked the question originally, you probably have already figured it out, but thank you for asking it. I bet there are other people who have the same questions.
Best regards
Heng
Hello Thandy Makgolane
DnaSP can also do the trick. Just upload your aligned fasta file on the software and export it as a nexus file. That's all.
Heng Liang sorry, the fasta file you are opening in MEGA has already been aligned previously in mega? with clustal or muscle?
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