cnxiaobo94

maybe you should set a env-path to psmc before using it, or use it as '/path/to/psmc/psmc - N25 - t15 - r5 - p" 4+25 * 2+4+6 "- o diploid.psmc...

the same needs for me! I obtained a contigs file with Megahit, but I want scaffolds. someone can help with this?

> It seems that MEGAHIT uses paired-end information to build contigs, but it does not output scaffold in the standard workflow. Is there a flag/ function to get MEGAHIT to...

> 1. I noticed that your miniconda3 used `ld` and `libgcc_s.so.1` from `base` environment, this way is not recommended. I created a new environment and compiled `msmc2` successful. Notice that...

> Looks to me like pop2 and pop3 are hardly diverged at all. Have you checked with other statistics, like FST, or looked at whether the population sizes start to...

> 这里没有看到报错。test模式需要-g输入基因树，从中抽取目标物种（一般-test指定3个以上内群，每次自动只取3个、加上外群，穷尽所有的组合），然后调用astral重新计算q1~q3，想以此简化3个以上物种错综复杂的关系。但实际这样也很难简化（有些情况可以），后面就基本放弃了这个模式。 哦哦 我后面重新从slidingwindowtree那一步开始，自己组合不同三个内群做了分析，但是在拓扑结构上会出现一些问题，可能因为减少的内群对拓扑结构有影响。比如原始内群结构是：（A，（B，C），（D，E）），但是我去掉E后，变成了（A，（B，（C,D）））而不是预期应该有的（A，（B，C）,D）），所以本来我是想看D和E对BC的节点，但是现在变成了B对CD的节点。

> Did you call SNPs from bam files? Perhaps genotype calling is skewed toward the reference genome due to reference bias. Using the outgroup as a reference genome is likely...