SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
CAP3 cygwin doesn't work. esiefker Bioinformatics 1 02-13-2018 11:10 AM
why doesn't this linux command work for me? wmseq Bioinformatics 4 11-08-2013 08:28 AM
mapdamage 2.0 doesn't work with paired ends Nihil347 Bioinformatics 1 09-16-2013 01:07 AM
BWA trim doesn’t work. CNVboy Bioinformatics 1 11-28-2011 02:57 AM
Soap2: the -w command doesn't work Yushan Hsiao Bioinformatics 0 08-10-2010 09:54 PM

Reply
 
Thread Tools
Old 07-22-2018, 05:45 PM   #1
ugurcabuk
Junior Member
 
Location: Turkey

Join Date: Jul 2018
Posts: 3
Exclamation The phylip doesn't work

I have been dealing with it for 4 hours. It still doesnt work and I will go crazy
It said that unexpected end-of-file. I want to use [B]dnadist.exe[B] I did it all as you see. What's wrong ?
Code:
	  26	   100
bra2      2325 2238 2252 6230 6786 6695 4550 6089 8677 6118 7902 6029 6974 4068 3431 3623 3503 4197 5082 3849 2816 3231 3165 3130 2741
bra4      2325 2206 2336 6366 6926 6933 4657 6256 8835 6264 8032 6188 7119 4218 3546 3810 3625 4359 5281 4018 2749 3201 3018 3004 2538
bra5      2238 2206 2202 6608 7210 7130 4823 6480 9150 6501 8314 6460 7393 4372 3705 3957 3809 4575 5500 4258 2813 3288 3124 3084 2514
bra6      2252 2336 2202 6446 6997 6896 4691 6300 8934 6298 8094 6247 7200 4254 3582 3833 3697 4420 5326 4079 2755 3234 3161 3015 2679
cer1      6230 6366 6608 6446 4859 4858 4724 4697 5689 4805 5493 4779 5072 4859 5063 4965 5051 4825 4649 4976 5832 5402 5581 5634 6591
cer3      6786 6926 7210 6997 4859 4972 5094 4969 5646 4871 5467 4739 5105 5302 5531 5304 5428 5161 4940 5359 6279 5880 6053 6137 7128
cer5      6695 6933 7130 6896 4858 4972 4964 4932 5553 4863 5542 4914 5147 5178 5467 5348 5499 5138 4948 5279 6288 5814 6121 6132 7090
cer6      4550 4657 4823 4691 4724 5094 4964 4659 6442 4736 5974 4631 5287 3967 3933 3868 3966 4051 4310 4067 4275 4130 4098 4250 4857
cer7      6089 6256 6480 6300 4697 4969 4932 4659 5759 4714 5572 4742 5077 4779 4985 4890 4944 4779 4727 4863 5761 5287 5551 5565 6470
fra1      8677 8835 9150 8934 5689 5646 5553 6442 5759 5702 5693 5748 5728 6499 6975 6799 6924 6446 6009 6595 8124 7506 7846 7849 9089
fra2      6118 6264 6501 6298 4805 4871 4863 4736 4714 5702 5415 4654 4947 4692 4956 4866 4899 4648 4566 4720 5772 5443 5567 5666 6517
fra3      7902 8032 8314 8094 5493 5467 5542 5974 5572 5693 5415 5413 5290 5782 6362 6236 6213 5682 5334 5872 7442 6984 7201 7289 8330
fra6      6029 6188 6460 6247 4779 4739 4914 4631 4742 5748 4654 5413 4962 4703 4893 4770 4813 4652 4572 4769 5711 5341 5491 5514 6409
fra7      6974 7119 7393 7200 5072 5105 5147 5287 5077 5728 4947 5290 4962 5227 5640 5535 5566 5198 4925 5345 6544 6212 6218 6395 7382
pub1      4068 4218 4372 4254 4859 5302 5178 3967 4779 6499 4692 5782 4703 5227 3352 3483 3283 3524 3887 3318 4050 3828 3997 3988 4608
pub2      3431 3546 3705 3582 5063 5531 5467 3933 4985 6975 4956 6362 4893 5640 3352 3190 3110 3525 4095 3184 3499 3348 3598 3491 4009
pub3      3623 3810 3957 3833 4965 5304 5348 3868 4890 6799 4866 6236 4770 5535 3483 3190 3257 3493 3969 3280 3651 3513 3724 3673 4233
pub4      3503 3625 3809 3697 5051 5428 5499 3966 4944 6924 4899 6213 4813 5566 3283 3110 3257 3438 4008 3320 3569 3421 3665 3543 4079
pub5      4197 4359 4575 4420 4825 5161 5138 4051 4779 6446 4648 5682 4652 5198 3524 3525 3493 3438 3849 3461 4158 3930 4155 4120 4781
pub6      5082 5281 5500 5326 4649 4940 4948 4310 4727 6009 4566 5334 4572 4925 3887 4095 3969 4008 3849 3827 5005 4706 4933 4920 5703
pub7      3849 4018 4258 4079 4976 5359 5279 4067 4863 6595 4720 5872 4769 5345 3318 3184 3280 3320 3461 3827 4017 3710 4019 3931 4587
tro2      2816 2749 2813 2755 5832 6279 6288 4275 5761 8124 5772 7442 5711 6544 4050 3499 3651 3569 4158 5005 4017 3139 2848 2947 2837
tro4      3231 3201 3288 3234 5402 5880 5814 4130 5287 7506 5443 6984 5341 6212 3828 3348 3513 3421 3930 4706 3710 3139 3301 2840 3382
tro5      3165 3018 3124 3161 5581 6053 6121 4098 5551 7846 5567 7201 5491 6218 3997 3598 3724 3665 4155 4933 4019 2848 3301 3123 2967
tro6      3130 3004 3084 3015 5634 6137 6132 4250 5565 7849 5666 7289 5514 6395 3988 3491 3673 3543 4120 4920 3931 2947 2840 3123 3050
tro7      2741 2538 2514 2679 6591 7128 7090 4857 6470 9089 6517 8330 6409 7382 4608 4009 4233 4079 4781 5703 4587 2837 3382 2967 3050
Please, help me
ugurcabuk is offline   Reply With Quote
Old 07-25-2018, 03:03 PM   #2
SNPsaurus
Registered Vendor
 
Location: Eugene, OR

Join Date: May 2013
Posts: 451
Default

A phylip file should have actual DNA sequence for each sample, shouldn't it?
http://scikit-bio.org/docs/0.2.3/gen...io.phylip.html
__________________
Providing nextRAD genotyping and PacBio sequencing services. http://snpsaurus.com
SNPsaurus is offline   Reply With Quote
Old 07-26-2018, 09:32 AM   #3
ugurcabuk
Junior Member
 
Location: Turkey

Join Date: Jul 2018
Posts: 3
Default

yeah you are right. After i checked it again, i solved it all. I just used false exe. I have to use another exe in the phylip that is called as neighbour.exe or sth like that. Thank you for response.
ugurcabuk is offline   Reply With Quote
Reply

Tags
distance, phylip, sequence alignment, tree

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 10:12 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO