From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from mp12.migadu.com ([2001:41d0:2:4a6f::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by ms5.migadu.com with LMTPS id 0KMlNB3H8GJ2aQAAbAwnHQ (envelope-from ) for ; Mon, 08 Aug 2022 10:19:41 +0200 Received: from aspmx1.migadu.com ([2001:41d0:2:4a6f::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by mp12.migadu.com with LMTPS id gBjyMx3H8GIsOQEAauVa8A (envelope-from ) for ; Mon, 08 Aug 2022 10:19:41 +0200 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by aspmx1.migadu.com (Postfix) with ESMTPS id 742B22A4F9 for ; Mon, 8 Aug 2022 10:19:41 +0200 (CEST) Received: from localhost ([::1]:54000 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1oKxzA-0005H8-3d for larch@yhetil.org; Mon, 08 Aug 2022 04:19:40 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:48736) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1oKxqo-0006iI-HH for guix-patches@gnu.org; Mon, 08 Aug 2022 04:11:02 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:49366) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1oKxqo-00033H-6t for guix-patches@gnu.org; Mon, 08 Aug 2022 04:11:02 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1oKxqo-0005yU-2d for guix-patches@gnu.org; Mon, 08 Aug 2022 04:11:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#56999] [PATCH 1/4] gnu: Add phyml. Resent-From: Ricardo Wurmus Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 08 Aug 2022 08:11:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 56999 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: To: =?UTF-8?Q?M=C4=83d=C4=83lin?= Ionel =?UTF-8?Q?Patra=C8=99cu?= Cc: 56999@debbugs.gnu.org Received: via spool by 56999-submit@debbugs.gnu.org id=B56999.165994625222947 (code B ref 56999); Mon, 08 Aug 2022 08:11:02 +0000 Received: (at 56999) by debbugs.gnu.org; 8 Aug 2022 08:10:52 +0000 Received: from localhost ([127.0.0.1]:39115 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1oKxqd-0005y3-KF for submit@debbugs.gnu.org; Mon, 08 Aug 2022 04:10:51 -0400 Received: from sender4-of-o50.zoho.com ([136.143.188.50]:21056) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1oKxqY-0005xq-NS for 56999@debbugs.gnu.org; Mon, 08 Aug 2022 04:10:50 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1659946242; cv=none; d=zohomail.com; s=zohoarc; b=V3E0ZCAsahI+cuwrlRRJUp1WzWjY6+KfhpHKlsTb63PD8zaGUybZg5SlKgfk1ofLV6nNB2VEmrmsABNcovPDEy7tfpYAjf3ZUfoHms7nC++MIHHqIHxw3bRSM0udSGZeYGMdMjMVePCZ/FTHGjbdarK8oIpBV1+Tuq3Uy8DOMDI= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1659946242; h=Content-Type:Content-Transfer-Encoding:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To; bh=Q1bXqGbErxjTQ9U1s3x+T26oN4095RXLUed6BDcVYUE=; b=h7dlx/2UeKPRi6O1otLr/sarXhlJceTl0d9CIw+w5JULtkqRQ9xKHBpggqJXxQ6z/r32fnCciQC7XtZel5nSzWWDzYhBiVZ6xowEHHD3SNAujvku5beqORLMk603suIm3SXkpc+m1UNS4FLTOnXcodD/Eu8Lto3fASFx2DBrlr4= ARC-Authentication-Results: i=1; mx.zohomail.com; dkim=pass header.i=elephly.net; spf=pass smtp.mailfrom=rekado@elephly.net; dmarc=pass header.from= DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1659946242; s=zoho; d=elephly.net; i=rekado@elephly.net; h=References:From:From:To:To:Cc:Cc:Subject:Subject:Date:Date:In-reply-to:Message-ID:MIME-Version:Content-Type:Content-Transfer-Encoding:Message-Id:Reply-To; bh=Q1bXqGbErxjTQ9U1s3x+T26oN4095RXLUed6BDcVYUE=; b=GjcM9SnlW7VuBfsjCdBFxyQngHZ1GadKRvab3/J9ABRV9wMgcXaMdWLheU3xqPs7 hgTR94eav/PnDz3gB+aXmdW1ysBO1asvw/9ALL0Tv9QbNCJplHjsv9+5d1inJidFJpD yLpaApg6TsZeZ8lLkdjTU8gIMGDaEiVosaTmlgX8= Received: from localhost (i5E862C12.versanet.de [94.134.44.18]) by mx.zohomail.com with SMTPS id 1659946239922474.4420415548036; Mon, 8 Aug 2022 01:10:39 -0700 (PDT) References: <398fc66441a34468a7c66370abb8f923@mdc-berlin.de> <20220805093306.21767-1-madalinionel.patrascu@mdc-berlin.de> User-agent: mu4e 1.8.7; emacs 28.1 From: Ricardo Wurmus Date: Mon, 08 Aug 2022 10:09:05 +0200 In-reply-to: <20220805093306.21767-1-madalinionel.patrascu@mdc-berlin.de> X-URL: https://elephly.net X-PGP-Key: https://elephly.net/rekado.pubkey X-PGP-Fingerprint: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC Message-ID: <875yj32m0z.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-ZohoMailClient: External X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+larch=yhetil.org@gnu.org Sender: "Guix-patches" X-Migadu-Flow: FLOW_IN X-Migadu-To: larch@yhetil.org X-Migadu-Country: US ARC-Message-Signature: i=2; a=rsa-sha256; c=relaxed/relaxed; d=yhetil.org; s=key1; t=1659946781; h=from:from:sender:sender:reply-to:subject:subject:date:date: message-id:message-id:to:to:cc:cc:mime-version:mime-version: content-type:content-type: content-transfer-encoding:content-transfer-encoding:resent-cc: resent-from:resent-sender:resent-message-id:in-reply-to:in-reply-to: references:references:list-id:list-help:list-unsubscribe: list-subscribe:list-post:dkim-signature; bh=Q1bXqGbErxjTQ9U1s3x+T26oN4095RXLUed6BDcVYUE=; b=ZoCDqJxv2Ujr4WcScpybarkmJDyarfjxQttbEnPFN/yGY7o7abBcmzrbpg2It+UkugvoNb zkeDIs9JcjZ9N/jD9Os1Wrni3AovAdrSJqy1ewaAWiDQhpgYpN2d96C6PaafS3qIcXFWPW 1Z0pUoXo4Ib5yioK+NX+zY6YRtP2kFiHzVm/Xyku/eczYohbn6Fgw/z1oXQ9YUH8uzJJuJ ndlbEqOJzM9IuUb9s7GzsKWb5wwfwm8/NxI6h3SbZfHtfUFhSLYSFz9Lemvub3xa3wcL6r +xmDkgYQTplOz9nFbtitAd8fD9mAi+VsXAF4vKHkS1YgZBfsxddgZJ3ubgdGAw== ARC-Seal: i=2; s=key1; d=yhetil.org; t=1659946781; a=rsa-sha256; cv=fail; b=gxpuJeuAcECaAh9A7azzfTSFHUzXWcUHeueQYLEp3UOWdYnkB/bq4JaFqTTQbh3h28WMK4 yT4V1wW8rPuoxx9fsEEwvo6zcvj8VrDe/uW6xPw/RljoWMi5X28NwNl1qkUu/wvmUpUxQH 7L1fbmsOaqEUvnIKJXgHPDA6WiySYCo31ITIS04ag/5+HDlXibvX1iBQ1+nMzxIC3nWsZY Gv3qQv6DcCQoq088FQE2IK9NoiYIYJ8L6FX7xLYo7OHHhWHH5rvZ61sQWhMAdF3Dqa9NKa wULIMmdy/yDcyoZ65IcYUcODgvbr8s5G/gkLR/BfiZGWZ8pKC5FH6LHMmbg9gw== ARC-Authentication-Results: i=2; aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=elephly.net header.s=zoho header.b=GjcM9Snl; arc=reject ("signature check failed: fail, {[1] = sig:zohomail.com:reject}"); dmarc=none; spf=pass (aspmx1.migadu.com: domain of "guix-patches-bounces+larch=yhetil.org@gnu.org" designates 209.51.188.17 as permitted sender) smtp.mailfrom="guix-patches-bounces+larch=yhetil.org@gnu.org" X-Migadu-Spam-Score: 3.61 Authentication-Results: aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=elephly.net header.s=zoho header.b=GjcM9Snl; arc=reject ("signature check failed: fail, {[1] = sig:zohomail.com:reject}"); dmarc=none; spf=pass (aspmx1.migadu.com: domain of "guix-patches-bounces+larch=yhetil.org@gnu.org" designates 209.51.188.17 as permitted sender) smtp.mailfrom="guix-patches-bounces+larch=yhetil.org@gnu.org" X-Migadu-Queue-Id: 742B22A4F9 X-Spam-Score: 3.61 X-Migadu-Scanner: scn1.migadu.com X-TUID: yZmzgaGpdpM9 M=C4=83d=C4=83lin Ionel Patra=C8=99cu = writes: > * gnu/packages/bioinformatics.scm (phyml): New variable. Thanks for the patch. > + "@code{PhyML} is a software package that uses modern statistical ap= proaches > +to analyse alignments of nucleotide or amino acid sequences in a phyloge= netic > +framework. The main tool in this package builds phylogenies under the m= aximum > +likelihood criterion. It implements a large number of substitution mode= ls coupled > +with efficient options to search the space of phylogenetic tree topologi= es. @code{ > +PhyTime} is another tool in the @code{PhyML} package that focuses on div= ergence > +date estimation in a Bayesian setting. The main strengths of @code{PhyT= ime} lie > +in its ability to accommodate for uncertrainty in the placement of fossil > +calibration and the use of realistic models of rate variation along the = tree. > +Finally, code{PhyREX} fits the spatial-Lambda-Fleming-Viot model to geo-= referenced > +genetic data. This model is similar to the structured coalescent but as= sumes that > +individuals are distributed along a spatial continuum rather than discre= te demes. > +@code{PhyREX} can be used to estimate population densities and rates of = dispersal. > +Its output can be processed by treeannotator (from the @code{BEAST} pack= age) as > +well as @code{SPREAD}.") The description mentions PhyTime and PhyREX, neither of which are included in this package. I=E2=80=99ll try to integrate this package with the definitions of phyml-mpi, phyml-phyrex, and phyml-rf that you=E2=80=99ve sent here. --=20 Ricardo