<html><head></head><body><div class="ydpd5c00a4byahoo-style-wrap" style="font-family:Helvetica Neue, Helvetica, Arial, sans-serif;font-size:13px;"><div><div dir="ltr" data-setdir="false">Thanks!</div><div><br></div><div class="ydpd5c00a4bsignature"><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 Tuesday, February 11, 2020, 12:08:25 a.m. GMT+7, Jean Lobry <jean.lobry@univ-lyon1.fr> wrote:
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<div><div dir="ltr">Yes, but you need an external program to make the<br clear="none">alignment, see for instance ?reverse.align<br clear="none"><br clear="none">Le 10/02/2020 à 17:22, Russell J Gray a écrit :<br clear="none">> I see.<br clear="none">> <br clear="none">> Is there any way to get distances for sequences without the same number <br clear="none">> of characters for all sequences?<br clear="none">> <br clear="none">> Best,<br clear="none">> <br clear="none">> -RG<br clear="none">> <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>><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<br clear="none">> <br clear="none">> <br clear="none">> <br clear="none">> <br clear="none">> On Monday, February 10, 2020, 09:29:54 p.m. GMT+7, Jean Lobry <br clear="none">> <<a shape="rect" ymailto="mailto:jean.lobry@univ-lyon1.fr" href="mailto:jean.lobry@univ-lyon1.fr">jean.lobry@univ-lyon1.fr</a>> wrote:<br clear="none">> <br clear="none">> <br clear="none">> 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> <br clear="none">> <mailto:<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> <br clear="none">> <mailto:<a shape="rect" ymailto="mailto:rgrayherpetology@gmail.com" href="mailto:rgrayherpetology@gmail.com">rgrayherpetology@gmail.com</a>>><br clear="none">> <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<br clear="none">> <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> <div class="yqt9570809399" id="yqtfd28128"><br clear="none">> <mailto:<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><br clear="none">> <br clear="none">> ><br clear="none">> <br clear="none"><br clear="none"></div></div></div>
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