Hi Swaraj,

Don't get fool. It happens quite a lot. It is a problem of the aligment format. TCS reads files in NEXUS or PHYLIP sequential formats. First, be sure TCS is reading an aligment, not just a file of sequences. Secondly, be sure the aligment is in nexus or phylip sequential format. TCS can not open "interleaved" formats. To change the format an useful online tool is: http://hcv.lanl.gov/content/sequence/FORMAT_CONVERSION/form.html

Best,

Hi Swaraj,

Don't get fool. It happens quite a lot. It is a problem of the aligment format. TCS reads files in NEXUS or PHYLIP sequential formats. First, be sure TCS is reading an aligment, not just a file of sequences. Secondly, be sure the aligment is in nexus or phylip sequential format. TCS can not open "interleaved" formats. To change the format an useful online tool is: http://hcv.lanl.gov/content/sequence/FORMAT_CONVERSION/form.html

Best,

Hey Swaraj,

I've just faced this same problem. I don't know why, but TCS can't read nexus of phylip files when you generate them by convertinf a fasta file using DNAsp or MEGA. But, things go fine when you use an online tool, e.g. http://sequenceconversion.bugaco.com/converter/biology/sequences/fasta_to_nexus.php

Unfortunatly, I just noticed your question dates from 2013...

Hope you found the answer on time.

All the best.

Hi there.. Thanks for the post. I had the same problem in TCS software as I used MEGA  TO CONVERT FAST FILE INTO NEXUS. i HOWEVER WANT TO KNOW is there any better way to represent this network. As I have got the network but it looks too clumsy.

Hi Ashwini, I usually redraw the network in powerpoint or excel as the TCS output is rather 'ugly' with a lot of extra connections. Have also redrawn in CorelDraw and photoshop though. It depends on the network complexity. If you'd prefer alternative software though, why not try NETWORK or HapStar? 

network is a good option

Hey thanks but problem with network software is I dont have software which is used to edit the network generated from this software as its not free as Network software

U can edit itself in NETWORK only, 

Hi,

you´re all probably through by now. Adding acomment for people from the future.

To convert fasta to nexus I used:

http://sequenceconversion.bugaco.com/converter/biology/sequences/fasta_to_nexus.php

TCS works very well after that.

I had an issue with a 2 kb alignment though. The website interleaved that big sequence and it does not provide a solution to that. I solved by:

1. using sequence matrix ( http://gaurav.github.io/taxondna/ ).

1.1 Where I dragged my sequence

1.2 Clicked "yes to all"

1.3 "Export"

1.4 "Export as NEXUS (non-interleaved)

2. Then, I used the website for sequence conversion (first link in my comment) and

2.1 opened this file (the one from the website) and copied the nexus header ( #NEXUS; begin data; dimensions ntax=79 nchar=1746; format datatype=dna missing=? gap=- ; matrix) ONTO the file originated in 1.4 --- IMPORTANT: replace the header.

3. If your sequence_IDs have spaces (" "), you have to replace them with underscores ("_").

This is a bit too much, but it took me a few hours massaging the data files to get this through. Sorry if it is confusing.

To make TCS more visual I used tcsBU.

https://github.com/sairum/tcsBU

It works really well. You just need a modern browser, load your TCS graphic and set colors.

Good Morning

Someone here could me help? I have no idea how can I save the image of haplotype net produced by TCS? How can I do that? Thanks a lot!!

I'm sure this has been resolved, but I thought I'd add my solution.

I have been using the free trial of CodonCode to align and check my sequences. From, here I can export my assembly as a single filed FASTA for analysis in R or as a sequential phylip (NOT NEXUS, this causes the error) for TCS.

Unfortunately Codon isn't free for long, but a month trial is more than required for trouble shooting these types of issues. Also I'm sure you could convert between formats using R, but that can be intimidating.