PhyloSuite

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GenBank file parse failed, please check your file carefully!

4

搜索NCBI导入gb文件时显示GenBank file parse failed, please check your file carefully! 报错信息如下： "Traceback (most recent call last): File "codes\src\handleGB.py", line 1648, in prepareGB File "codes\src\handleGB.py", line 1183, in fetchAllIndex File "codes\src\handleGB.py", line...

zzzzzhaozhuang

The program encountered an unforeseen problem

5

when the software is open, or I click the "check for update" button, this msg appears

ywzhan2

运行Partitionfinder2时出错

1

尊敬的张老师： 在运行Partitionfinder2时，第52循环提示存在以下错误： ERROR | 2023-05-22 19:56:21,154 | main | A program that Partitionfinder uses failed. Output follows, in case it's helpful for finding the problem ERROR | 2023-05-22 19:56:21,154 |...

wangyan48691412

IQ-TREE and ML-TREE

1

老师，就是如果我跑ML树的话，就是在ModelFinder中建模型的时候，model for 那里我要选择PhyML对吧？ 然后再把ModelFinder_results导入import to IQ-TREE,最后跑出来的树就是ML树对吧？

CXna1108

Mrbayes error

4

老师，关于以下存储空间不足和字符报错一般怎么解决？ Division 1 has 708 unique site patterns Initializing conditional likelihoods Using standard non-SSE likelihood calculator for division 1 (single-precision) Out of memory. Most probable cause for the problem is...

CXna1108

Alignment-Characters Issues

1

老师，您好。对序列进行比对时出现了以下问题，这里报错的意思时序列里面含有特殊字符吗？我检查了所有序列，里面没有特殊字符，对于这种情况，我应该如何解决这个问题？ 还有，如果没有解决以下报错问题的话，我把这些序列在其他软件(geneious)进行比对后，再到phylosuite跑树的话还会报错吗？ Gap Penalty = -1.53, +0.00, +0.00 === Alphabet 'i' is unknown. === Please check site 1 in sequence 9497. === To make an alignment that has unusual characters...

CXna1108

Taxon name Issues

4

老师，又来打扰您啦。就是我在跑树的时候出现了以下报错： **Taxon name** AB614504_1_Phyllocnistis_gracilistylella_mitochondrial_COI_gene_for_cytochrome_oxidase_subunit_I__partial_cds__country__Japan_Nagano__Nagano__Sai_gawa is too long. Maximun 99 characters is allowed. 由于我的序列较多，许多Taxon name的字符也很长，因此，我想问问老师有没有什么办法可以批量的将‘Taxon name'批量更改为只保留序列的序列号/登录号，而序列号/登录号后面的描述删除呢？ 也给出了相对应的解决方案： 1.Deleting previously defined characters 2.Deleting previously defined taxa 还有以下的提示 Returning execution to command line......

CXna1108

PhyloSuit Viewer Issues

2

1.老师您好。想问一下，就是将比对好的序列在PhyloSuit Viewer界面打开后，序列的某些部分是.......（点点点），这代表什么意思？是没有序列的意思吗？没有有序列的区域因该显示的是------这些符号吧？ 2.还有没有序列的区域，在最上方的*****这些符号又是什么意思呢？

CXna1108

For information: HmmCleaner.pl cannot be installed.

2

It seems the current version of HmmCleaner.pl cannot be installed - the cpan testers log shows zero successes. I always get the error below where it asks for Bio::MUST:: Drivers...

theo-allnutt-bioinformatics

Question about mrbayes block

2

Hello, great bioinformatic suite, congrats I have a question, I have my own results from modelfinder (from a cluster), and I want to import those results to PhyloSuite for get...

luishdez35