Re: [Biopython] Struggling with MSA...
Peter Cock <[email protected]> Thu, 15 Feb 2024 16:02:06 +0000
| Newsgroups | gmane.comp.python.bio.general |
|---|---|
| Message-ID | <CAKVJ-_5iwNasB4pgTZ1fb-RVuz9NicQkFRD3DUN+La5_OyCgWA@mail.gmail.com> |
U29ycnkgeWVzLCBJIHVzZWQgdGhpcyBhcyBhIHRocmVzaG9sZCBmb3IgaWYgYSBjb2x1bW4gd2Fz IGdhcHB5LCBhbmQKbGlrZWx5IHRvIGJlIGluIHRoZSBtb2RlbCBvciBub3Q6CgphbWlub19hY2lk cy5nZXQoIi0iLCAwKSA8IGxlbihhbGlnbikqMC41CgpNaWdodCBuZWVkIHRvIHVzZSA8PSB0byBt YXRjaCwgb3IgcGVyaGFwcyB0aGV5IHVzZSBhIG1vcmUKc29waGlzdGljYXRlZCBjcml0ZXJpYS4K ClBldGVyCgpPbiBUaHUsIEZlYiAxNSwgMjAyNCBhdCAzOjU24oCvUE0gRGFuIEJvbHNlciA8ZGFu LmJvbHNlckBvdXRzZWUuY28udWs+IHdyb3RlOgo+Cj4gU29ycnksIGJ5ICdoYWxmIGdhcHMnIEkg dGhvdWdodCB5b3UgbWVhbnQgYSBzcGVjaWZpYyB0aGluZywgbGlrZSwgImxvb2sgYXQgdGhhdCBo YWxmIGdhcCEiLiBJIGd1ZXNzIHlvdSBtZWFuLCBjb2x1bW5zIHdoZXJlIGhhbGYgb2YgdGhlIHZh bHVlcyBpbiB0aGUgY29sdW1uIGFyZSBnYXBzLgo+Cj4gTG9va2luZyBkaXJlY3RseSBhdCB0aGUg YWxpZ25tZW50LCBJIGd1ZXNzIHRoZXJlIGlzIG5vIHdheSB0byB3b3JrIG91dCBwcmVjaXNlbHkg d2hpY2ggY29sdW1ucyBhcmUgZ2FwcyBvciBub3QgaW4gdGhlIG1vZGVsPwo+Cj4KPgo+Cj4KPgo+ IE9uIFRodSwgMTUgRmViIDIwMjQgYXQgMTU6NDcsIERhbiBCb2xzZXIgPGRhbi5ib2xzZXJAb3V0 c2VlLmNvLnVrPiB3cm90ZToKPj4KPj4gSGkgUGV0ZXIsCj4+Cj4+IE9uIFRodSwgMTUgRmViIDIw MjQgYXQgMTU6MjgsIFBldGVyIENvY2sgPHAuai5hLmNvY2tAZ29vZ2xlbWFpbC5jb20+IHdyb3Rl Ogo+Pj4KPj4+IEhlbGxvIERhbiwKPj4+Cj4+PiBJdCB0aGF0IGlzIGEgcHJvYmFiaWxpdHkgYXQg dGhlIGVuZCwgeW91IGhhdmUgdGhlIHdyb25nIGRlbm9taW5hdG9yIC0KPj4+IHNob3VsZCBiZSBs ZW4oYWxpZ24pID09IHN1bShhbWlub19hY2lkcy52YWx1ZXMoKQo+Pgo+Pgo+PiBNYWtlcyBubyBk aWZmZXJlbmNlLCB0aGV5IGFyZSB0aGUgc2FtZSAoaW5jbHVkaW5nIC1zKS4gVGhlIHByb2ZpbGUg cmVwb3J0cyAtcyBhcyAnSW5zZXJ0IFByb2JhYmlsaXR5Jy4KPj4KPj4KPj4+IE5vdGUgdGhpcyBz ZWVkIGFsaWdubWVudCBoYXMgMTY0IGNvbHVtbnMsIHlldCB0aGUgbW9kZWwgcGFnZSBzYXlzIHRo ZQo+Pj4gbW9kZWwgaGFzIDk1IGNvbHVtbnMuIElmIEkgY291bnQgdGhlIG51bWJlciBvZiBjb2x1 bW5zIHdoaWNoIGFyZSBoYWxmCj4+PiBnYXBzIHRoYXQncyBwcmV0dHkgY2xvc2UuLi4KPj4KPj4K Pj4gSSBkb24ndCB1bmRlcnN0YW5kIHdoYXQgdGhhdCBtZWFucyBvciBpbXBsaWVzLi4uIElzIHNv bWV0aGluZyB3cm9uZyBzb21ld2hlcmU/Cj4+Cj4+Cj4+IENoZWVycywKPj4gRGFuLgo+Pgo+Pgo+ Pj4gUGV0ZXIKPj4+Cj4+PiBPbiBUaHUsIEZlYiAxNSwgMjAyNCBhdCAzOjA54oCvUE0gRGFuIEJv bHNlciA8ZGFuLmJvbHNlckBvdXRzZWUuY28udWs+IHdyb3RlOgo+Pj4gPgo+Pj4gPiBIaSwKPj4+ ID4KPj4+ID4gU29ycnksIEkgY2FuJ3QgZm9sbG93IHRoZSBkb2NzIChvciBmaW5kIHRoZSByaWdo dCBkb2NzKS4KPj4+ID4KPj4+ID4gSSd2ZSBnb3QgdGhlICdzZWVkJyBzdG9ja2hvbG0gYWxpZ25t ZW50IGZvciB0aGlzIGRvbWFpbjoKPj4+ID4gaHR0cHM6Ly93d3cuZWJpLmFjLnVrL2ludGVycHJv L2VudHJ5L3BmYW0vUEYwODI0MS9lbnRyeV9hbGlnbm1lbnRzLz90eXBlPXNlZWQKPj4+ID4KPj4+ ID4gYW5kIEknbSB0cnlpbmcgdG8gcmVwcm9kdWNlIHRoZSBzaWduYXR1cmUgaXQgc2hvd3MgaGVy ZToKPj4+ID4gaHR0cHM6Ly93d3cuZWJpLmFjLnVrL2ludGVycHJvL2VudHJ5L3BmYW0vUEYwODI0 MS9sb2dvLwo+Pj4gPgo+Pj4gPiBJJ20gbm90IHN1cmUgYSkgd2h5IHRoZSBwcm9iYWJpbGl0aWVz IGRpZmZlciBpbiB0aGUgcHJvZmlsZSByZWxhdGl2ZSB0byB0aGUgc2VlZCBhbGlnbm1lbnQsIG9y IGIpIGhvdyB0byBmaWx0ZXIgY29sdW1ucyBpbiB0aGUgYWxpZ25tZW50IGJ5IHRob3NlIHRoYXQg aGF2ZSBhIG1hdGNoIGluIHRoZSBtb2RlbCAoc2VlIGNvbHVtbnMgNC02IGluIHRoZSBhbGlnbm1l bnQsIHdoaWNoIGFyZSBnYXBzIGluIHRoZSBtb2RlbCkuCj4+PiA+Cj4+PiA+IEkgdGhpbmsgaWYg SSBjYW4gYW5zd2VyIGIpIHRoZW4gdGhlIGFuc3dlciB0byBhKSB3aWxsIGJlLCAibG9vayBhdCB0 aGUgZnVsbCBhbGlnbm1lbnQiLgo+Pj4gPgo+Pj4gPiBIZXJlIGlzIG15IGNydWRlICdiZXN0IGd1 ZXNzJyBjb2RlOgo+Pj4gPgo+Pj4gPiBpbXBvcnQgZ3ppcAo+Pj4gPiBpbXBvcnQgQmlvLkFsaWdu SU8KPj4+ID4KPj4+ID4gIyBtc2EgPSAiUEYwODI0MS5hbGlnbm1lbnQuZnVsbC5neiIKPj4+ID4g bXNhID0gIlBGMDgyNDEuYWxpZ25tZW50LnNlZWQuZ3oiCj4+PiA+Cj4+PiA+IHdpdGggZ3ppcC5v cGVuKG1zYSwgInJ0IikgYXMgaGFuZGxlOgo+Pj4gPiBhbGlnbiA9IEJpby5BbGlnbklPLnJlYWQo aGFuZGxlLCAic3RvY2tob2xtIikKPj4+ID4gbmNvbHMgPSBhbGlnbi5nZXRfYWxpZ25tZW50X2xl bmd0aCgpCj4+PiA+Cj4+PiA+IGZvciBjb2wgaW4gcmFuZ2UobmNvbHMpOgo+Pj4gPiBhbWlub19h Y2lkcyA9IGRpY3QoKQo+Pj4gPiBmb3IgcyBpbiBhbGlnbls6LCBjb2xdOgo+Pj4gPiBhbWlub19h Y2lkc1tzXSA9IGFtaW5vX2FjaWRzLmdldChzLCAwKSArIDEKPj4+ID4gcHJpbnQoYW1pbm9fYWNp ZHMpCj4+PiA+IGZvciBzIGluIGFtaW5vX2FjaWRzOgo+Pj4gPiBwcmludChmIntzfToge2FtaW5v X2FjaWRzW3NdOjNkfSB7YW1pbm9fYWNpZHNbc10gLyBsZW4oYWxpZ24pOi4zZn0iKQo+Pj4gPgo+ Pj4gPgo+Pj4gPgo+Pj4gPiBJIGhhdmUgdGhlIGZlZWxpbmcgSSdtIGRvaW4gaXQgcm9uZy4uLgo+ Pj4gPgo+Pj4gPiBUaGUgYWJvdmUgaXMganVzdCBhICd3YXJtIHVwJywgcmVhbGx5IEkgd2FudCB0 byBzZWUgdGhlIGNvbnNlcnZhdGlvbiBzY29yZSwgYmFzZSBieSBiYXNlIG9uIGEgZ2l2ZW4gcHJv dGVpbiBpbiB0aGUgYWxpZ25tZW50ICh3aGVyZSBpdCBtYXRjaGVzIHRoZSBtb2RlbCkuCj4+PiA+ Cj4+PiA+IE1hbnkgdGhhbmtzIGZvciBhbnkgc3VnZ2VzdGlvbnMsIGFuZCBzb3JyeSBmb3Igbm90 IGJlaW5nIGFibGUgdG8gZmluZCB0aGUgcmlnaHQgZG9jdW1lbnQgdG8gYW5zd2VyIHRoZXNlIHF1 ZXN0aW9ucy4KPj4+ID4KPj4+ID4KPj4+ID4ga3RoeGJpLAo+Pj4gPiBEYW4uCj4+PiA+IF9fX19f X19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fCj4+PiA+IEJpb3B5dGhv biBtYWlsaW5nIGxpc3QgIC0gIEJpb3B5dGhvbkBiaW9weXRob24ub3JnCj4+PiA+IGh0dHBzOi8v bWFpbG1hbi5vcGVuLWJpby5vcmcvbWFpbG1hbi9saXN0aW5mby9iaW9weXRob24KX19fX19fX19f X19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX18KQmlvcHl0aG9uIG1haWxpbmcg bGlzdCAgLSAgQmlvcHl0aG9uQGJpb3B5dGhvbi5vcmcKaHR0cHM6Ly9tYWlsbWFuLm9wZW4tYmlv Lm9yZy9tYWlsbWFuL2xpc3RpbmZvL2Jpb3B5dGhvbgo=