<html><head></head><body><div class="ydp19d3844ayahoo-style-wrap" style="font-family: Helvetica Neue, Helvetica, Arial, sans-serif; font-size: 13px;"><div><div dir="ltr" data-setdir="false">I see.<br><br>Is there any way to get distances for sequences without the same number of characters for all sequences?</div><div dir="ltr" data-setdir="false"><br></div><div dir="ltr" data-setdir="false">Best,</div><div dir="ltr" data-setdir="false"><br></div><div dir="ltr" data-setdir="false">-RG</div><div dir="ltr" data-setdir="false"><br></div><div dir="ltr" data-setdir="false"><br></div><div><br></div><div class="ydp19d3844asignature"><div style="font-family:Helvetica, Arial, sans-serif;font-size:13px;"><div class="ydp6fa35b7pasted-link"><div style="color:rgb(100, 100, 100);font-family:Arial;font-size:12px;margin-bottom:5px;margin-top:0px !important;"><b>--</b></div><div style="color:rgb(100, 100, 100);font-family:Arial;font-size:12px;margin-bottom:5px;margin-top:0px !important;"><b>Russell J. Gray</b><br>Wildlife Ecology & Conservation Consultant</div><table width="470" border="0" cellspacing="0" cellpadding="0" style="color:rgb(100, 100, 100);font-family:Arial;font-size:12px;width:470px;margin-top:5px;"><tbody><tr><td style="font-family:Roboto, RobotoDraft, Helvetica, Arial, sans-serif;margin:0px;color:rgb(141, 141, 141);"><p style="margin:0px;">0934581341 <span style="color:rgb(69, 102, 142);display:inline-block;">|</span> <span style="display:inline-block;"><a href="mailto:rgrayherpetology@gmail.com" style="color:rgb(141, 141, 141);text-decoration-line:underline;font-family:sans-serif;" rel="nofollow" target="_blank">rgrayherpetology@gmail.com</a></span></p></td></tr><tr><td style="font-family:Roboto, RobotoDraft, Helvetica, Arial, sans-serif;margin:0px;color:rgb(141, 141, 141);"><p style="margin:0px;"><span style="white-space:nowrap;display:inline-block;"><a href="https://www.rjgrayecology.com/" style="color:rgb(141, 141, 141);text-decoration-line:underline;font-family:sans-serif;" rel="nofollow" target="_blank">https://www.rjgrayecology.com/</a></span></p></td></tr><tr><td style="font-family:sans-serif;margin:0px;color:rgb(141, 141, 141);"><span style="display:inline-block;">705 alligator ranch rd. New Smyrna Beach, FL, USA. 32168</span></td></tr></tbody></table></div><br></div></div></div>
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On Monday, February 10, 2020, 09:29:54 p.m. GMT+7, Jean Lobry <jean.lobry@univ-lyon1.fr> wrote:
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<div><div dir="ltr">A problem here is that the file "Amanita.txt" does<br clear="none">not contain an alignment since the number of characters<br clear="none">is not the same for all sequences :<br clear="none"><br clear="none"> > library(seqinr)<br clear="none"> > dna <- read.alignment("Amanita.txt", format = "fasta")<br clear="none"> > unlist(lapply(dna$seq, nchar))<br clear="none"> [1] 626 625 639 687 646 676 670 517 497 770 720 713 730 563 540<br clear="none"> ><br clear="none"><br clear="none">Le 10/02/2020 à 05:56, Russell J Gray a écrit :<br clear="none">> Hi there,<br clear="none">> <br clear="none">> I'm trying to use the seqinr package for some ITS sequence analysis and <br clear="none">> when I run the first basic functions of the package it automatically <br clear="none">> crashes R. I've attached my FASTA text file, and have copied my code <br clear="none">> here....<br clear="none">> Once you run the line "*D <- dist.alignment(dna, matrix = <br clear="none">> "similarity")*" if you try to view the dna data, or if R autocompletes a <br clear="none">> function, or you try to do anything further, R runs the "Fatal Error" <br clear="none">> window and says it cannot connect to the server.<br clear="none">> <br clear="none">> <br clear="none">> *library(seqinr)*<br clear="none">> *library(adegenet)*<br clear="none">> *library(ape)*<br clear="none">> *library(ggtree)*<br clear="none">> *<br clear="none">> *<br clear="none">> *<br clear="none">> *<br clear="none">> *dna <- read.alignment("Amanita.txt", format = "fasta")*<br clear="none">> *D <- dist.alignment(dna, matrix = "similarity")*<br clear="none">> *<br clear="none">> *<br clear="none">> <br clear="none">> Any help is appreciated!<br clear="none">> <br clear="none">> Best regards<br clear="none">> <br clear="none">> -RG<br clear="none">> <br clear="none">> <br clear="none">> *--*<br clear="none">> *Russell J. Gray*<br clear="none">> Wildlife Ecology & Conservation Consultant<br clear="none">> <br clear="none">> 0934581341 | <a shape="rect" ymailto="mailto:rgrayherpetology@gmail.com" href="mailto:rgrayherpetology@gmail.com">rgrayherpetology@gmail.com</a> <mailto:<a shape="rect" ymailto="mailto:rgrayherpetology@gmail.com" href="mailto:rgrayherpetology@gmail.com">rgrayherpetology@gmail.com</a>><div class="yqt0084847726" id="yqtfd61709"><br clear="none">> <br clear="none">> <a shape="rect" href="https://www.rjgrayecology.com/" target="_blank">https://www.rjgrayecology.com/</a><br clear="none">> <br clear="none">> 705 alligator ranch rd. New Smyrna Beach, FL, USA. 32168</div><br clear="none">> <br clear="none">> <br clear="none">> <br clear="none">> _______________________________________________<br clear="none">> Seqinr-forum mailing list<br clear="none">> <a shape="rect" ymailto="mailto:Seqinr-forum@lists.r-forge.r-project.org" href="mailto:Seqinr-forum@lists.r-forge.r-project.org">Seqinr-forum@lists.r-forge.r-project.org</a><br clear="none">> <a shape="rect" href="https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/seqinr-forum" target="_blank">https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/seqinr-forum</a><div class="yqt0084847726" id="yqtfd58375"><br clear="none">> <br clear="none"><br clear="none"></div></div></div>
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