Ed Davis

FYI there is another LoveIT based theme that has fuse.js implemented: https://github.com/HEIGE-PCloud/DoIt

Thanks for this issue. I was running into the same problem and didn't realize that it was due to gap characters. I'll remove the gaps and try again. Having a...

I have the same error: ``` # davised:Linux @ vaughan in /local/cluster [13:50:24] C:1 $ which -a bwa-mem2 /local/cluster/bwa-mem2/bwa-mem2 # davised:Linux @ vaughan in /local/cluster [13:50:40] $ bwa-mem2 ERROR: prefix...

> Simply edit the utils.h file (lines 53 and 60) and remove the two uses of "void" inside the parenthesis where the __rdtsc macro is defined. This will remove all...

I can provide the original files, but any -p prefix.nex file with the * syntax works to produce this output.

Thanks! I'll remove the * from now on.

Hi Minh, Maybe I wasn't clear. Here is the output when I run `iqtree2 -s AAK85942.1.aln -m MFP` ``` $ cat AAK85942.1.aln.uniqueseq.phy 4 649 Sinorhizobium_meliloti_BM806 MAKVIGIDLGTTNSCVSVMDGKDAKVIENAEGARTTPSMVAFTEDGERLVGQPAKRQAVTNPENTLFAIKRLIGRTFEDPTTQKDKGMVPYKIVKADNGDAWVEAHGTSYSPSQISAMILQKMKETAESYLGEKVEKAVITVPAYFNDAQRQATKDAGKIAGLDVLRIINEPTAAALAYGLDKKEGKTIAVYDLGGGTFDISVLEIGDGVFEVKSTNGDTFLGGEDFDMRLVEYLASEFKKEQGIDLKNDKLALQRLKEAAEKAKIELSSSQQTEINLPFITADASGPKHLTMKLSRAKFESLVEDLIQKTIAPCKAALKDAGVSAAEIDEVVLVGGMTRMPKVQETVKQLFGKEPHKGVNPDEVVAMGAAIQAGVLQGDVKDVLLLDVTPLSLGIETLGGVFTRLIERNTTIPTKKSQVFSTADDNQSAVTIRVSQGEREMAADNKLLGQFDLVGIPPAPRGVPQIEVTFDIDANGIVQVSAKDKGTGKEHQIRIQASGGLSDAEIEKMVKDAEANAEADKKRREGVEAKNQAESLVHSSEKSLQEHGDKVSETDRKAIEDAIAALKSAVEVSEPDAEDIKAKTNTLMEVSMKLGQAIYEAQQT--DAA--HADAAA-DAKR--S-GDDVVDADYEEVKDEDDRKRSA Sinorhizobium_meliloti_USDA1022 MAKVIGIDLGTTNSCVSVMDGKDAKVIENAEGARTTPSMVAFTEDGERLVGQPAKRQAVTNPENTLFAIKRLIGRTFEDPTTQKDKGMVPYKIVKADNGDAWVEAHGTSYSPSQISAMILQKMKETAESYLGEKVEKAVITVPAYFNDAQRQATKDAGKIAGLDVLRIINEPTAAALAYGLDKKEGKTIAVYDLGGGTFDISVLEIGDGVFEVKSTNGDTFLGGEDFDMRLVEYLASEFKKEQGIDLKNDKLALQRLKEAAEKAKIELSSSQQTEINLPFITADASGPKHLTMKLSRAKFESLVEDLIQKTIAPCKAALKDAGVSAAEIDEVVLVGGMTRMPKVQETVKQLFGKEPHKGVNPDEVVAMGAAIQAGVLQGDVKDVLLLDVTPLSLGIETLGGVFTRLIERNTTIPTKKSQVFSTADDNQSAVTIRVSQGEREMAADNKLLGQFDLVGIPPAPRGVPQIEVTFDIDANGIVQVSAKDKGTGKEHQIRIQASGGLSDAEIEKMVKDAEANAEADKKRREGVEAKNQAESLVHSSEKSLQEHGDKVSETDRKAIEDAIAALKSAVEVSEPDAEDIKAKTNTLMEVSMKLGQAIYEAQQT--DAA--HADAAA-DAKR--S-GDDVVDADYEEVKDEDDRKRSA Rhizobium_leguminosarum_bv._viciae_CZP1G1 MAKVIGIDLGTTNSCVAVMDGKDAKVIENAEGARTTPSMVAFSDDGERLVGQPAKRQAVTNPTNTLFAVKRLIGRRYEDPTVEKDKHLVPFTIVKGDNGDAWVEANGKGYSPAQISAMILQKMKETAESYLGEKVEKAVITVPAYFNDAQRQATKDAGRIAGLEVLRIINEPTAAALAYGLDKKEGKTIAVYDLGGGTFDISILEIGDGVFEVKSTNGDTFLGGEDFDMRLVEYLVAEFKRDNGIDLKNDKLALQRLKEAAEKAKIELSSSQQTEINLPFITADASGPKHLTLKLTRAKLESLVDDLVQRTIAPCKAALKDAGVTAAEIDEVVLVGGMSRMPKVQEVVKQLFGKEPHKGVNPDEVVALGAAIQAGVLQGDVKDVLLLDVTPLSLGIETLGGVFTRLIERNTTIPTKKSQTFSTAEDNQQAVTIRVSQGEREMAADNKLLGQFDLVGLPPSPRGMPQIEVTFDIDANGIVQVSAKDKGTGKEQQIRIQASGGLSDADIEKMVKDAEAHATEDKKRREAVEARNQAESLIHSSEKSLKDYGDKVSEADRTAISDAIAALKTASEASEPDADDIKAKTQTLMEVSMKLGQAIYEAQQA--ESG-AAGDASA-E-----G-GDNVVDADYEEIKD-DDRKKSA...

If this is intended, why is the output different when specifying a file with `-p file.nex` compared to `-s file.aln`?

I ran the emboss pepstats and the composition is the same between the alignments, of course! You might make a note in the documentation somewhere that the partitioned alignments are...

One other thought I had would be allow specification of the zip file itself to the rehydrate function. You could easily unzip the file and get the directory structure that...