Re: [Biopython] Struggling with MSA...
"marek.schwarz" <[email protected]> Sat, 17 Feb 2024 08:24:38 +0100
| Newsgroups | gmane.comp.python.bio.general |
|---|---|
| Message-ID | <[email protected]> |
SGksCnRoZXJlIGFyZSBweXRob24gYmluZGluZ3MgZm9yIHRoZSBITU1FUjMgYyBsaWJyYXJ5IAoo aHR0cHM6Ly9naXRodWIuY29tL2FsdGhvbm9zL3B5aG1tZXIpLCB0aGlzIGNvdWxkIGJlIG9mIGlu dGVyZXN0IHRvIHlvdSAKaWYgeW91IHdhbnQgdG8gaW5zcGVjdCB0aGUgYWN0dWFsIG1vZGVsIGl0 c2VsZi4KCkJlc3QKTWFyZWsKClBzLjogTm90IGFmZmlsaWF0ZWQgd2l0aCB0aGUgbGlicmFyeSBu b3IgdGhlIEhNTUVSLgoKRG5lIDIwMjQtMDItMTYgMTE6NTksIERhbiBCb2xzZXIgbmFwc2FsOgo+ IEkgZG9uJ3Qgc3VwcG9zZSB0aGVyZSBpcyBhIHBhY2thZ2UgZm9yIHJlYWRpbmcgaW4gdGhlIEhN TT8g8J+YhQo+IAo+IE9uIFRodSwgMTUgRmViIDIwMjQgYXQgMTY6MTgsIERhbiBCb2xzZXIgPGRh bi5ib2xzZXJAb3V0c2VlLmNvLnVrPgo+IHdyb3RlOgo+IAo+PiBSZWNyZWF0aW5nIHRoZSBwcm9m aWxlIHdhcyBqdXN0IGEgc2FuaXR5IGNoZWNrLiBSZWFsbHkgSSB3YW50IHRvCj4+IGxvb2sgYXQg Y29uc2VydmF0aW9uIGFjcm9zcyB0aGUgcHJvdGVpbiBvZiBpbnRlcmVzdC4KPj4gCj4+IE9uIFRo dSwgMTUgRmViIDIwMjQgYXQgMTY6MTMsIFBldGVyIENvY2sgPHAuai5hLmNvY2tAZ29vZ2xlbWFp bC5jb20+Cj4+IHdyb3RlOgo+PiAKPj4+IFlvdSBtYXkgaGF2ZSBtb3JlIGpveSBzdGFydGluZyBm cm9tIHRoZSBITU0gZm9yIHRoZSBtb2RlbD8KPj4+IAo+Pj4gCj4+IAo+IGh0dHBzOi8vd3d3LmVi aS5hYy51ay9pbnRlcnByby93d3dhcGkvL2VudHJ5L3BmYW0vUEYwODI0MT9hbm5vdGF0aW9uPWht bQo+Pj4gCj4+PiBQZXRlcgo+Pj4gCj4+PiBPbiBUaHUsIEZlYiAxNSwgMjAyNCBhdCA0OjA24oCv UE0gRGFuIEJvbHNlcgo+Pj4gPGRhbi5ib2xzZXJAb3V0c2VlLmNvLnVrPiB3cm90ZToKPj4+PiAK Pj4+PiBTZWFyY2hpbmcgSE1NRVIgZ2l2ZXMgbWUgKGNyeXB0aWM/KSBkZXRhaWxzIG9mIHRoZSBt b2RlbCBtYXRjaDoKPj4+PiAKPj4+PiBGYW1pbHktSWQgRmFtaWx5LUFjY2Vzc2lvbiBDbGFuIFN0 YXJ0IEVuZCBBbGktU3RhcnQgQWxpLUVuZAo+Pj4gTW9kZWwtU3RhcnQgTW9kZWwtRW5kIEJpdC1T Y29yZSBJbmQuLUUtdmFsdWUgQ29uZC4tRS12YWx1ZQo+Pj4gRGVzY3JpcHRpb24KPj4+PiAKPj4+ IAo+PiAKPiA9PT09PT09PT09PT09PT09PT09PT09PT09PT09PT09PT09PT09PT09PT09PT09PT09 PT09PT09PT09PT09PT09PT09PT09PT09PT09PT09PT09PT09PT09PT09PT09PT09PT09PT09PT09 PT09PT09PT09PT09PT09PT09PT09PT09Cj4+Pj4gCj4+Pj4gTWV0aHlsdHJhbnNmXzExIFBGMDgy NDEuMTUgQ0wwMDYzIDYzIDE3MyA2MyAxNzIgMSA5NSA1MS4zMAo+Pj4gMS41ZS0xMyAzLjFlLTE3 IE1ldGh5bHRyYW5zZmVyYXNlIGRvbWFpbgo+Pj4+IAo+Pj4+IAo+Pj4gCj4+IAo+IC0tLS0tLS0t LS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0t LS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0t LS0tLS0tLQo+Pj4+IAo+Pj4+IE1PREVMCj4+PiAKPj4gCj4gTGR2R2NHdEdybGFlYWxha3JnLmFy dnZndkRsc2tlbWxrbGFrZWthc2VlZ2xrdmVmdnZhZGFla2xwZmVkbnNmRGx2dnNzZXZsaGh2Li4u ZS4uLi4uLi4uLi4uLmRwZWthbGtlaWFSdkxrcGdHbGx2Cj4+Pj4gTUFUQ0ggIEwgK0djRysgK2wr ICtsICAgZyAgK3YrIHZEK3MgICsrKysgKysrICAgICsgKysrKyAgK2QrK2tsCj4+PiBmKysrc2ZE K3YrICsgK2wrICsgICBlICAgICAgICAgICAgICsrKytsK2UrIFJ2TCBwZ0crKysKPj4+PiBQUEwK Pj4+IAo+PiAKPiA1NjkqKioqKioqKioqKio3Nzc5KioqKioqKioqKioqKjc3NzY2NjY2NjY2LjY5 KioqKioqKioqKioqKioqKioqKioqKioqKioqKio4NjYyNjY3Nzc4ODg4ODg4KioqKioqKioqKioq KioqKioqOTcKPj4+PiBTRVEKPj4+IAo+PiAKPiBMVkxHQ0dOU0FMU1lFTEZMR0dmUE5WVFNWRFlT U1ZWVkFBTVFBUkhBSFZQLVFMUldFVE1EVlJLTERGUFNBU0ZEVlZMRUtHVExEQUxsYWdFcmRwd3R2 c3NlZ3ZoVFZEUVZMU0VWU1JWTFZQR0dSRkkKPj4+PiAKPj4+PiAKPj4+PiBTbyBJIGd1ZXNzIGl0 J3MgcG9zc2libGUgdG8gd29yayBiYWNrd2FyZHMgZnJvbSB0aGVyZS4uLgo+Pj4+IAo+Pj4+IAo+ Pj4+IAo+Pj4+IE9uIFRodSwgMTUgRmViIDIwMjQgYXQgMTY6MDIsIFBldGVyIENvY2sKPj4+IDxw LmouYS5jb2NrQGdvb2dsZW1haWwuY29tPiB3cm90ZToKPj4+Pj4gCj4+Pj4+IFNvcnJ5IHllcywg SSB1c2VkIHRoaXMgYXMgYSB0aHJlc2hvbGQgZm9yIGlmIGEgY29sdW1uIHdhcwo+Pj4gZ2FwcHks IGFuZAo+Pj4+PiBsaWtlbHkgdG8gYmUgaW4gdGhlIG1vZGVsIG9yIG5vdDoKPj4+Pj4gCj4+Pj4+ IGFtaW5vX2FjaWRzLmdldCgiLSIsIDApIDwgbGVuKGFsaWduKSowLjUKPj4+Pj4gCj4+Pj4+IE1p Z2h0IG5lZWQgdG8gdXNlIDw9IHRvIG1hdGNoLCBvciBwZXJoYXBzIHRoZXkgdXNlIGEgbW9yZQo+ Pj4+PiBzb3BoaXN0aWNhdGVkIGNyaXRlcmlhLgo+Pj4+PiAKPj4+Pj4gUGV0ZXIKPj4+Pj4gCj4+ Pj4+IE9uIFRodSwgRmViIDE1LCAyMDI0IGF0IDM6NTbigK9QTSBEYW4gQm9sc2VyCj4+PiA8ZGFu LmJvbHNlckBvdXRzZWUuY28udWs+IHdyb3RlOgo+Pj4+Pj4gCj4+Pj4+PiBTb3JyeSwgYnkgJ2hh bGYgZ2FwcycgSSB0aG91Z2h0IHlvdSBtZWFudCBhIHNwZWNpZmljIHRoaW5nLAo+Pj4gbGlrZSwg Imxvb2sgYXQgdGhhdCBoYWxmIGdhcCEiLiBJIGd1ZXNzIHlvdSBtZWFuLCBjb2x1bW5zIHdoZXJl Cj4+PiBoYWxmIG9mIHRoZSB2YWx1ZXMgaW4gdGhlIGNvbHVtbiBhcmUgZ2Fwcy4KPj4+Pj4+IAo+ Pj4+Pj4gTG9va2luZyBkaXJlY3RseSBhdCB0aGUgYWxpZ25tZW50LCBJIGd1ZXNzIHRoZXJlIGlz IG5vIHdheSB0bwo+Pj4gd29yayBvdXQgcHJlY2lzZWx5IHdoaWNoIGNvbHVtbnMgYXJlIGdhcHMg b3Igbm90IGluIHRoZSBtb2RlbD8KPj4+Pj4+IAo+Pj4+Pj4gCj4+Pj4+PiAKPj4+Pj4+IAo+Pj4+ Pj4gCj4+Pj4+PiAKPj4+Pj4+IE9uIFRodSwgMTUgRmViIDIwMjQgYXQgMTU6NDcsIERhbiBCb2xz ZXIKPj4+IDxkYW4uYm9sc2VyQG91dHNlZS5jby51az4gd3JvdGU6Cj4+Pj4+Pj4gCj4+Pj4+Pj4g SGkgUGV0ZXIsCj4+Pj4+Pj4gCj4+Pj4+Pj4gT24gVGh1LCAxNSBGZWIgMjAyNCBhdCAxNToyOCwg UGV0ZXIgQ29jawo+Pj4gPHAuai5hLmNvY2tAZ29vZ2xlbWFpbC5jb20+IHdyb3RlOgo+Pj4+Pj4+ PiAKPj4+Pj4+Pj4gSGVsbG8gRGFuLAo+Pj4+Pj4+PiAKPj4+Pj4+Pj4gSXQgdGhhdCBpcyBhIHBy b2JhYmlsaXR5IGF0IHRoZSBlbmQsIHlvdSBoYXZlIHRoZSB3cm9uZwo+Pj4gZGVub21pbmF0b3Ig LQo+Pj4+Pj4+PiBzaG91bGQgYmUgbGVuKGFsaWduKSA9PSBzdW0oYW1pbm9fYWNpZHMudmFsdWVz KCkKPj4+Pj4+PiAKPj4+Pj4+PiAKPj4+Pj4+PiBNYWtlcyBubyBkaWZmZXJlbmNlLCB0aGV5IGFy ZSB0aGUgc2FtZSAoaW5jbHVkaW5nIC1zKS4gVGhlCj4+PiBwcm9maWxlIHJlcG9ydHMgLXMgYXMg J0luc2VydCBQcm9iYWJpbGl0eScuCj4+Pj4+Pj4gCj4+Pj4+Pj4gCj4+Pj4+Pj4+IE5vdGUgdGhp cyBzZWVkIGFsaWdubWVudCBoYXMgMTY0IGNvbHVtbnMsIHlldCB0aGUgbW9kZWwKPj4+IHBhZ2Ug c2F5cyB0aGUKPj4+Pj4+Pj4gbW9kZWwgaGFzIDk1IGNvbHVtbnMuIElmIEkgY291bnQgdGhlIG51 bWJlciBvZiBjb2x1bW5zCj4+PiB3aGljaCBhcmUgaGFsZgo+Pj4+Pj4+PiBnYXBzIHRoYXQncyBw cmV0dHkgY2xvc2UuLi4KPj4+Pj4+PiAKPj4+Pj4+PiAKPj4+Pj4+PiBJIGRvbid0IHVuZGVyc3Rh bmQgd2hhdCB0aGF0IG1lYW5zIG9yIGltcGxpZXMuLi4gSXMKPj4+IHNvbWV0aGluZyB3cm9uZyBz b21ld2hlcmU/Cj4+Pj4+Pj4gCj4+Pj4+Pj4gCj4+Pj4+Pj4gQ2hlZXJzLAo+Pj4+Pj4+IERhbi4K Pj4+Pj4+PiAKPj4+Pj4+PiAKPj4+Pj4+Pj4gUGV0ZXIKPj4+Pj4+Pj4gCj4+Pj4+Pj4+IE9uIFRo dSwgRmViIDE1LCAyMDI0IGF0IDM6MDnigK9QTSBEYW4gQm9sc2VyCj4+PiA8ZGFuLmJvbHNlckBv dXRzZWUuY28udWs+IHdyb3RlOgo+Pj4+Pj4+Pj4gCj4+Pj4+Pj4+PiBIaSwKPj4+Pj4+Pj4+IAo+ Pj4+Pj4+Pj4gU29ycnksIEkgY2FuJ3QgZm9sbG93IHRoZSBkb2NzIChvciBmaW5kIHRoZSByaWdo dCBkb2NzKS4KPj4+Pj4+Pj4+IAo+Pj4+Pj4+Pj4gSSd2ZSBnb3QgdGhlICdzZWVkJyBzdG9ja2hv bG0gYWxpZ25tZW50IGZvciB0aGlzIGRvbWFpbjoKPj4+Pj4+Pj4+IAo+Pj4gCj4+IAo+IGh0dHBz Oi8vd3d3LmViaS5hYy51ay9pbnRlcnByby9lbnRyeS9wZmFtL1BGMDgyNDEvZW50cnlfYWxpZ25t ZW50cy8/dHlwZT1zZWVkCj4+Pj4+Pj4+PiAKPj4+Pj4+Pj4+IGFuZCBJJ20gdHJ5aW5nIHRvIHJl cHJvZHVjZSB0aGUgc2lnbmF0dXJlIGl0IHNob3dzIGhlcmU6Cj4+Pj4+Pj4+PiBodHRwczovL3d3 dy5lYmkuYWMudWsvaW50ZXJwcm8vZW50cnkvcGZhbS9QRjA4MjQxL2xvZ28vCj4+Pj4+Pj4+PiAK Pj4+Pj4+Pj4+IEknbSBub3Qgc3VyZSBhKSB3aHkgdGhlIHByb2JhYmlsaXRpZXMgZGlmZmVyIGlu IHRoZQo+Pj4gcHJvZmlsZSByZWxhdGl2ZSB0byB0aGUgc2VlZCBhbGlnbm1lbnQsIG9yIGIpIGhv dyB0byBmaWx0ZXIKPj4+IGNvbHVtbnMgaW4gdGhlIGFsaWdubWVudCBieSB0aG9zZSB0aGF0IGhh dmUgYSBtYXRjaCBpbiB0aGUgbW9kZWwKPj4+IChzZWUgY29sdW1ucyA0LTYgaW4gdGhlIGFsaWdu bWVudCwgd2hpY2ggYXJlIGdhcHMgaW4gdGhlIG1vZGVsKS4KPj4+Pj4+Pj4+IAo+Pj4+Pj4+Pj4g SSB0aGluayBpZiBJIGNhbiBhbnN3ZXIgYikgdGhlbiB0aGUgYW5zd2VyIHRvIGEpIHdpbGwgYmUs Cj4+PiAibG9vayBhdCB0aGUgZnVsbCBhbGlnbm1lbnQiLgo+Pj4+Pj4+Pj4gCj4+Pj4+Pj4+PiBI ZXJlIGlzIG15IGNydWRlICdiZXN0IGd1ZXNzJyBjb2RlOgo+Pj4+Pj4+Pj4gCj4+Pj4+Pj4+PiBp bXBvcnQgZ3ppcAo+Pj4+Pj4+Pj4gaW1wb3J0IEJpby5BbGlnbklPCj4+Pj4+Pj4+PiAKPj4+Pj4+ Pj4+ICMgbXNhID0gIlBGMDgyNDEuYWxpZ25tZW50LmZ1bGwuZ3oiCj4+Pj4+Pj4+PiBtc2EgPSAi UEYwODI0MS5hbGlnbm1lbnQuc2VlZC5neiIKPj4+Pj4+Pj4+IAo+Pj4+Pj4+Pj4gd2l0aCBnemlw Lm9wZW4obXNhLCAicnQiKSBhcyBoYW5kbGU6Cj4+Pj4+Pj4+PiBhbGlnbiA9IEJpby5BbGlnbklP LnJlYWQoaGFuZGxlLCAic3RvY2tob2xtIikKPj4+Pj4+Pj4+IG5jb2xzID0gYWxpZ24uZ2V0X2Fs aWdubWVudF9sZW5ndGgoKQo+Pj4+Pj4+Pj4gCj4+Pj4+Pj4+PiBmb3IgY29sIGluIHJhbmdlKG5j b2xzKToKPj4+Pj4+Pj4+IGFtaW5vX2FjaWRzID0gZGljdCgpCj4+Pj4+Pj4+PiBmb3IgcyBpbiBh bGlnbls6LCBjb2xdOgo+Pj4+Pj4+Pj4gYW1pbm9fYWNpZHNbc10gPSBhbWlub19hY2lkcy5nZXQo cywgMCkgKyAxCj4+Pj4+Pj4+PiBwcmludChhbWlub19hY2lkcykKPj4+Pj4+Pj4+IGZvciBzIGlu IGFtaW5vX2FjaWRzOgo+Pj4+Pj4+Pj4gcHJpbnQoZiJ7c306IHthbWlub19hY2lkc1tzXTozZH0g e2FtaW5vX2FjaWRzW3NdIC8KPj4+IGxlbihhbGlnbik6LjNmfSIpCj4+Pj4+Pj4+PiAKPj4+Pj4+ Pj4+IAo+Pj4+Pj4+Pj4gCj4+Pj4+Pj4+PiBJIGhhdmUgdGhlIGZlZWxpbmcgSSdtIGRvaW4gaXQg cm9uZy4uLgo+Pj4+Pj4+Pj4gCj4+Pj4+Pj4+PiBUaGUgYWJvdmUgaXMganVzdCBhICd3YXJtIHVw JywgcmVhbGx5IEkgd2FudCB0byBzZWUgdGhlCj4+PiBjb25zZXJ2YXRpb24gc2NvcmUsIGJhc2Ug YnkgYmFzZSBvbiBhIGdpdmVuIHByb3RlaW4gaW4gdGhlCj4+PiBhbGlnbm1lbnQgKHdoZXJlIGl0 IG1hdGNoZXMgdGhlIG1vZGVsKS4KPj4+Pj4+Pj4+IAo+Pj4+Pj4+Pj4gTWFueSB0aGFua3MgZm9y IGFueSBzdWdnZXN0aW9ucywgYW5kIHNvcnJ5IGZvciBub3QgYmVpbmcKPj4+IGFibGUgdG8gZmlu ZCB0aGUgcmlnaHQgZG9jdW1lbnQgdG8gYW5zd2VyIHRoZXNlIHF1ZXN0aW9ucy4KPj4+Pj4+Pj4+ IAo+Pj4+Pj4+Pj4gCj4+Pj4+Pj4+PiBrdGh4YmksCj4+Pj4+Pj4+PiBEYW4uCj4+Pj4+Pj4+PiBf X19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fXwo+Pj4+Pj4+Pj4g QmlvcHl0aG9uIG1haWxpbmcgbGlzdCAgLSAgQmlvcHl0aG9uQGJpb3B5dGhvbi5vcmcKPj4+Pj4+ Pj4+IGh0dHBzOi8vbWFpbG1hbi5vcGVuLWJpby5vcmcvbWFpbG1hbi9saXN0aW5mby9iaW9weXRo b24KPiBfX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fXwo+IEJp b3B5dGhvbiBtYWlsaW5nIGxpc3QgIC0gIEJpb3B5dGhvbkBiaW9weXRob24ub3JnCj4gaHR0cHM6 Ly9tYWlsbWFuLm9wZW4tYmlvLm9yZy9tYWlsbWFuL2xpc3RpbmZvL2Jpb3B5dGhvbgoKClVwb3pv cm5lbmk6Ck5lbmktbGkgdiB0ZXRvIHpwcmF2ZSB2eXNsb3ZuZSB1dmVkZW5vIGppbmFrLCBtYSB0 YXRvIEUtbWFpbG92YSB6cHJhdmEgbmVibyBqZWppIHByaWxvaHkgcG91emUgaW5mb3JtYXRpdm5p IGNoYXJha3Rlci4gVGF0byB6cHJhdmEgYW5pIGplamkgcHJpbG9oeSB2IHphZG5lbSBvaGxlZHUg dXN0YXZ5IEFWIENSLCB2LnYuaS4gayBuaWNlbXUgbmV6YXZhenVqaS4gVGV4dCB0ZXRvIHpwcmF2 eSBuZWJvIGplamljaCBwcmlsb2ggbmVuaSBuYXZyaGVtIG5hIHV6YXZyZW5pIHNtbG91dnksIGFu aSBwcmlqZXRpbSBwcmlwYWRuZWhvIG5hdnJodSBuYSB1emF2cmVuaSBzbWxvdXZ5LCBhbmkgamlu eW0gcHJhdm5pbSBqZWRuYW5pbSBzbWVydWppY2ltIGsgdXphdnJlbmkgamFrZWtvbGl2IHNtbG91 dnkgYSBuZXpha2xhZGEgcHJlZHNtbHV2bmkgb2Rwb3ZlZG5vc3QgdXN0YXZ1IEFWIENSLCB2LnYu aS4KCkRpc2NsYWltZXI6CklmIG5vdCBleHByZXNzbHkgc3RhdGVkIG90aGVyd2lzZSwgdGhpcyBl LW1haWwgbWVzc2FnZSAoaW5jbHVkaW5nIGFueSBhdHRhY2hlZCBmaWxlcykgaXMgaW50ZW5kZWQg cHVyZWx5IGZvciBpbmZvcm1hdGlvbmFsIHB1cnBvc2VzIGFuZCBkb2VzIG5vdCByZXByZXNlbnQg YSBiaW5kaW5nIGFncmVlbWVudCBvbiB0aGUgcGFydCBvZiBJbnN0aXR1dGVzIG9mIHRoZSBDemVj aCBBY2FkZW15IG9mIFNjaWVuY2VzLiBUaGUgdGV4dCBvZiB0aGlzIG1lc3NhZ2UgYW5kIGl0cyBh dHRhY2htZW50cyBjYW5ub3QgYmUgY29uc2lkZXJlZCBhcyBhIHByb3Bvc2FsIHRvIGNvbmNsdWRl IGEgY29udHJhY3QsIG5laXRoZXIgdGhlIGFjY2VwdGFuY2Ugb2YgYSBwcm9wb3NhbCB0byBjb25j bHVkZSBhIGNvbnRyYWN0LCBub3IgYW55IG90aGVyIGxlZ2FsIGFjdCBsZWFkaW5nIHRvIGNvbmNs dWRpbmcgYW55IGNvbnRyYWN0OyBub3IgZG9lcyBpdCBjcmVhdGUgYW55IHByZS1jb250cmFjdHVh bCBsaWFiaWxpdHkgb24gdGhlIHBhcnQgb2YgSW5zdGl0dXRlcyBvZiB0aGUgQ3plY2ggQWNhZGVt eSBvZiBTY2llbmNlcy4KX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19f X19fX18KQmlvcHl0aG9uIG1haWxpbmcgbGlzdCAgLSAgQmlvcHl0aG9uQGJpb3B5dGhvbi5vcmcK aHR0cHM6Ly9tYWlsbWFuLm9wZW4tYmlvLm9yZy9tYWlsbWFuL2xpc3RpbmZvL2Jpb3B5dGhvbgo=