$./phylophlan.py -u mygenomes when finished, the resulting tree will appear in the output/mygenomes folder. Example 1: Corynebacterium 'de novo' phylogenetic tree building You can try out this operation ( -u) using an example included in the PhyloPhlAn package you downloaded called examplecorynebacteria and stored in the input folder. In contains a protein multifasta file for each of the 30 genomes available for the as February 2012 plus two genomes as a meaningful outgroup. As mentioned above, the command for obtaining the phylogenetic tree is. $./phylophlan.py -u examplecorynebacteria -nproc 4 Using 4 threads (specified with -nproc 4) this operation should take no more than 4-5 minutes, but even using one processor only (default) should give you the results in 10 minutes or so. In the output/examplecorynebacteria/ folder you'll find a file of the resulting tree as provided by, and a file containing the same tree rerooted with a procedure which tries to maximize the distance from the root to any leaf. The two files are available for download (, and can be inspected with and drawn with.
Figure 3B in the reports and discuss this example. Also the full three of life reported above has been originally generated in this way. Notice that the concatenated alignment used to generate the tree with FastTree is stored in data/examplecorynebacteria/aln.fna and can be used as input for other phylogenetic reconstruction software such as or among. Inserting new genomes to the tree of life PhyloPhlAn let you insert a genome (or a set of genomes) into the already built microbial tree of life (containing 3,000 genomes, see figure and tree files above). Also in this case you need to create a dedicated folder (e.g. Mygenomestoinsert) in the input folder to store the protein multifasta files of interest. The command is.
$./phylophlan.py -i mygenomestoinsert -nproc 16 If possible, we would recommend to use as many threads as possible ( -nproc) because this operation is quite computationally demanding as it requires the alignments with other 3,000 genomes to be updated and the full tree of life to be rebuilt. The resulting tree file output/mygenomestoinsert/mygenomestoinsert.tree.int.nwk can be inspected with tree visualization software to check where the new genomes are rooted and their relations with already well characterized strains. Example 2: inserting Lactobacillus and Sulfolobus genomes into the tree of life As an example of insertion, we included in the input folder contained in the PhyloPhlAn package, three genomes recently sequenced and not yet included into the PhyloPhlAn tree and repository. These are two and one genomes available in IMG (accessions, and respectively). $./phylophlan.py -i exampleinsertion -nproc 16 The resulting file exampleinsertion.tree.int.nwk now contains the thousands of genomes in the PhyloPhlAn repository as well as the three 'new' genomes. Imputing taxonomic labels for newly integrated genomes You can also ask PhyloPhlAn to try to automatically assign a taxonomic labels to the genomes integrated into the tree of life ( -i option introduced above).
Mapa De Guatemala.pdf. Similar searches. Mapa De Guatemala Guatemala Mapa S K Mapa Mapa SK Mapa Mexico D.f. Mapa Sk Mapa Solution Venezuela Mapa Mapa De Nicaragua Bolivia Mapa Mapa De Venezuela Cuba Mapa R Dominicana Mapa Ecuador Mapa Mapa Bus Barcelona. Excellent software for educational purposes. Useful improvement I would like see in a future version: permit the user to set the letter repertoire and order for variables. Examples: C, B, A instead A,B,C; N,M,L instead A,B,C.
This is possible simply adding the -t flag (for taxonomic analysis) to the same command line. $./phylophlan.py -i -t mygenomestoinsert -nproc 16 In addition to the output/mygenomestoinsert/mygenomestoinsert.tree.int.nwk file, you will obtain tab-separated text files with the most confident taxonomic predictions for your genomes in the output/mygenomestoinsert/ folder. Example 3: predicting the taxonomic labels of three 'new' genomes Suppose you don't know the taxonomic labels of the Lactobacillus and Sulfolobus genomes used as examples above, possibly because of insufficient phenotipic characterization or because you obtained them with metagenomic assembly. You can call the PhyloPhlAn taxonomic imputation pipeline as. $./phylophlan.py -i -t exampleinsertion -nproc 16 And check the predictions in the file that we report below: SulfolobusacidocaldariusN8 dArchaea.pCrenarchaeota.cThermoprotei.oSulfolobales.fSulfolobaceae.gSulfolobus.s?t? LactobacillusrhamnosusKATCC8530 dBacteria.pFirmicutes.cBacilli.oLactobacillales.fLactobacillaceae.gLactobacillus.srhamnosus.t? LactobacillusrhamnosusLRHMDP3 dBacteria.pFirmicutes.cBacilli.oLactobacillales.fLactobacillaceae.gLactobacillus.srhamnosus.t?
As expected, the all three genomes are assigned to the right genera. The two lactobacilli could also be assigned to the right species ( srhamnosus) whereas PhyloPhlAn does not find enough support to assign the Sulfolobus genome to the 'acidocaldarius' species. All command line options and parameters $./phylophlan.py -h usage: phylophlan.py -h -i -u -t -taxtest TAXTEST -c -cleanall -nproc N -v PROJECT NAME NAME AND VERSION: PhyloPhlAn version 0.99 (8 May 2013) AUTHORS: Nicola Segata ([email protected]) and Curtis Huttenhower ([email protected]) DESCRIPTION PhyloPhlAn is a computational pipeline for reconstructing highly accurate and resolved phylogenetic trees based on whole-genome sequence information. The pipeline is scalable to thousands of genomes and uses the most conserved 400 proteins for extracting the phylogenetic signal. PhyloPhlAn also implements taxonomic curation, estimation, and insertion operations.
Positional arguments: PROJECT NAME The basename of the project corresponding to the name of the input data folder inside input/. The input data consist of a collection of multifasta files (extension.faa) containing the proteins in each genome. If the project already exists, the already executed steps are not re-ran.
The results will be stored in a folder with the project basename in output/ Multiple project can be generated and they safetely coexists. Optional arguments: -h, -help show this help message and exit -i, -integrate Integrate user genomes into the PhyloPhlAn tree -u, -usertree Build a phylogenetic tree using user genomes only -t, -taxonomicanalysis Check taxonomic inconsistencies and refine/correct taxonomic labels -taxtest TAXTEST nerrors:type:taxl:tmin:tex:name (alpha version, experimental!) -c, -clean Clean the final and partial data produced for the specified project. (use -cleanall for removing general installation and database files) -cleanall Remove all instalation and database file leaving untouched the initial compressed data that is automatically extracted and formatted at the first pipeline run.
Projects are not remove (specify a project and use -c for removing projects).nproc N The number of CPUs to use for parallelizing the blasting default 1, i.e.
Mermaid Fountain, built by Diego de Porres in 1737, Antigua Guatemala central square. The first building of a cathedral was begun in 1545 with the debris brought from the destroyed settlement in the valley of Almolonga; however, its construction was hampered by frequent earthquakes throughout the years. The city was the final resting place of the great Spanish chronicler, and his remains were interred in one of the churches that was eventually ruined by earthquakes. The construction of the royal houses for the residence of the Captain General and the members of the started in 1558; the complex also included the Royal Treasury, jail, Army quarters, the Hall of Arms, and the housing of Audiencia members. In the sixteenth century, there were several important earthquakes on the following dates:. March 21, 1530.
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September 11, 1541. 1565 (exact date unknown). 1575 (exact date unknown). November 30, 1577. December 23, 1585 In 1566 King Felipe II of Spain gave it the title of 'Muy Noble y Muy Leal' ('Very Noble and Very Loyal'). 17th-century events. Antigua, Guatemala.
Church damaged by an earthquake The strongest earthquakes experienced by the city of Santiago de los Caballeros before its final move in 1776 were the in 1717. At that time, the power of the over the Spanish Empire's citizens was absolute and any natural disaster was considered as divine punishment. In the city, people also believed that the proximity of the (English: Volcano of Fire) was the cause of earthquakes; the great architect Diego de Porres even said that all the earthquakes were caused by volcano explosions. On August 27 there was a strong eruption of, which lasted until August 30; the residents of the city asked for help to Santo Cristo of the Cathedral and to the Virgen del Socorro who were sworn patrons of the. On August 29, a Virgen del Rosario procession took to the streets after a century without leaving her temple, and there were many more holy processions until 29 September, the day of San Miguel.
Early afternoon earthquakes were minor, but at about 7:00 p.m. There was a strong earthquake that forced residents to leave their homes; tremors and rumblings followed until four o'clock. The neighbors took to the streets and loudly confessed their sins, bracing for the worst.
The San Miguel earthquake damaged the city considerably, to the point that some rooms and walls of the Royal Palace were destroyed. There was also a partial abandonment of the city, food shortages, lack of manpower, and extensive damage to the city infrastructure, not to mention numerous dead and injured. These earthquakes made the authorities consider moving to a new city less prone to seismic activity. City residents strongly opposed the move, and even took to the Royal Palace in protest; in the end, the city did not move, but the number of troops of the Army Battalion required to maintain order was considerable. The damage to the palace were repaired by Diego de Porres, who finished repairs in 1720, although there are indications that there were additional work done by Porres until 1736. San Casimiro earthquake On March 4, 1751, the destroyed the city of Santiago de Guatemala once more.
The church roof of the fell to the ground, forcing the Jesuits once again to ask for help from the parishioners to rebuild. Once again, the building was among the most beautiful in the city when the repairs were completed. In fact, a period of prosperity began after the San Casimiro earthquake, as the city saw major improvements such as street embellishment and the introduction of a tap water system. A new City Hall was built, and on July 17, 1753, work on the Jesuit plaza in front of the church was finished. Santa Marta earthquake.
Postmark ANTIGUA CANCELADO in 1887, after Guatemala joined the UPU. Note the Quetzal.
After the independence of Guatemala from Spain in 1821, the Jesuit complex became public property once again and was in several lawsuits that lasted until 1829, when the and the conservative were expelled from Central America after the invasion of liberal general and the establishment of a secular government. The new liberal government decreed that all the confiscated Catholic church possessions had to be turned into elementary schools and university classrooms. As of 1850, Antigua had an estimated population of 9,000. And by 1865, the building was functioning as a vapor activated thread mill, but it was not profitable due to a lack of expert technicians and raw material; and by 1872, the Jesuits were once again expelled from Guatemala by the liberal regime of. In 1884 City Hall made an announcement that it intended to transform the old Society of Jesus buildings into a market, in spite of the strong opposition from the neighbors that already had small shops on the plaza. It was until 1912 that a market was placed in the complex. 20th-century events.
A poor native family living in the ruins of, as described by prince in 1920. In April 1920, during the very last days of regime, prince visited Antigua Guatemala and wrote about his impressions of the city in his book Between two continents. His book is an objective description of the terrible conditions the road and the ruins used to be in: 'For some little way outside Guatemala City it was a fairly decent car ride, but then the roads began developing sand drifts, and later, of tumbled stone as two years earlier, the country had been devastated by and government corruption made the recovery impossible'. 'The hills grew steeper and steeper, the jolting more pronounced and the stones even sharper; besides, on top of the road was a two-foot layer of dust which hid the pitfalls but did not detract from their effect'. 'Along the way, they passed long lines of Indians on their way to Guatemala City, carrying their heavy burdens with apparent ease; men, women and children carried something in the way of a load, and they all carried it quickly. With respect to traffic, it was almost non-existent, aside from mule-pulled wagons'. After passing Mixco, the road proceeded more steeply upward, with a precipitous drop on one side and sheer cliff rising on the other; here and there a cross stood by the wayside, marking the spot where some traveler had died.
After reaching the highest point, they started down towards Antigua. The city was in sight when a person in uniform planted himself in front of the car; it turned out to be the city commandant, along with six soldiers with wooden guns. Compared to Guatemala City at the time, Antigua was quite nicely kept, although all the churches were equally dilapidated and left entirely to themselves, as rebuilding since 1773 was confined to the strictly necessary.
For the most part, only blank walls and shattered domes remained to greet the visitor by 1920, and some of the churches were in pitiful conditions. In Santa Clara, for example, a mule was grazing, and in the Church of Grace a native family had taken up its quarters, along with their varied collection of domestic animals. But there were other monuments in decent shape:. The Escuela de Cristo was one of the best preserved churches and the most picturesque at the time, given that it was united with a convent that was still standing. The priest that received the Prince and his three companions told them that all the silver and gold from the church had already been sold by his predecessors, so that he, to his extreme regret, was unable to sell any to them. The old monastery with its many underground passages from the monks' cells to those of the nuns was worth a visit, especially one part where the cells were built in a circle surrounding a central common chamber.
Antigua Guatemala in the 21st century. In the former Metropolitan Cathedral of Santiago. Central Park – Parque Central – is the heart of the city, with the reconstructed fountain there acting as a popular gathering spot. To the north of the Central Park is the Arco de Santa Catalina, one of the most recognizable architectural landmarks of Antigua. La Antigua is noted for its very elaborate religious celebrations during , leading up to ( Semana Santa) and ( Pascua). Each Sunday during Lent, one of the local sponsors a through the streets of Antigua. Elaborate and beautiful artistic carpets, predominantly made of dyed sawdust, flowers, pine needles, and even fruits and vegetables, adorn the processions' paths.
Due to its popularity among tourists and its very well-developed tourism infrastructure, Antigua Guatemala is often used as a central location from which to visit other tourist areas in Guatemala and Central America. Cruise ships that dock at Guatemalan ports offer trips to Antigua from both the Pacific and Atlantic. Antigua also holds a sizeable retirement community of expatriates from the US and Europe. Economy Historically, the area was considered to be one of the finest agriculturally in Guatemala. Tourism is the main driver of the economy.
Antigua is also a coffee-producing region of. Tourists visiting Antigua, 2005 Language schools Antigua is known as a destination for people who want to learn Spanish through immersion.
There are many Spanish language schools in Antigua, and it is one of the most popular and best recognized centers for Spanish language study by students from Europe, Asia, and North America. Language institutes are one of the primary industries of Antigua, along with tourism. Sports football club has played in the Guatemala top division for several years, but have been playing in the second division lately. Their home stadium is the, which has a capacity of 9,000.
They are nicknamed Los panzas verdes ('Green bellies'). Cuisine There are many restaurants in Antigua.
Small eateries can be found at the Antigua marketplace next to the central bus stop, where you will find traditional Guatemalan dishes such as the traditional/ breakfast, for example: refried beans, fried egg, fried plantain, and fresh cheese, served with handmade. Throughout Antigua you can find many cuisines from around the world: Mediterranean, Italian, Asian, American, and even British pies and French pastries! Film locations for. In 1935, the film, was filmed on location in Guatemala, taking advantage of the help from the and president.
The places where the filming was made were:.: scenes of a native town where the explorers first met. Antigua Guatemala: The Green Goddess temple.: arrival and departure of the boats carrying the explorers.: jungle scenes.: Mayan city where they get lectured on the.: then luxurious Palace Hotel was used to shoot the scenes of the hotel in the imaginary town of At Mantique The Border: 1982. This square was also called 'Plaza Mayor', 'Plaza Real' and 'Plaza de Armas'.
Previously the audience was in the city of 'Gracias a Dios' in Honduras, but there it lacked the appropriate conditions for its activities. The Audiencia was called 'of the Confines' because it was within the confines of.
Parts of this construction are still preserved and may be the only ruins dating from the 16th century in the city of Antigua Guatemala. The chocolate was the drink of choice in Guatemala during the colonial era. It was considered a liquid food. During the Spanish colony, 'General Study' was another name for the universities. i.e., Local authorities chosen among the. Royal emissaries from the Spanish Crown.
References.
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